N E X T F L O W ~ version 21.04.3 Launching `nf-core-rnaseq-3.3/workflow/main.nf` [high_sammet] - revision: 366f959333 ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/rnaseq v3.3 ------------------------------------------------------ Core Nextflow options runName : high_sammet containerEngine : singularity launchDir : /nobackup/tomato_genome/nfcore2 workDir : /nobackup/tomato_genome/nfcore2/work projectDir : /nobackup/tomato_genome/nfcore2/nf-core-rnaseq-3.3/workflow userName : aloraine profile : singularity configFiles : /nobackup/tomato_genome/nfcore2/nf-core-rnaseq-3.3/workflow/nextflow.config Input/output options input : samples.csv Reference genome options fasta : S_lycopersicum_Sep_2019.fa gtf : S_lycopersicum_Sep_2019.gtf gene_bed : S_lycopersicum_Sep_2019.bed Institutional config options custom_config_base: /nobackup/tomato_genome/nfcore2/nf-core-rnaseq-3.3/workflow/../configs/ !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/rnaseq for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.1400710 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md ------------------------------------------------------ [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE - [- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC - [- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE - [- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC - [- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE - [- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC - [- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES - [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE - [- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC - [- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS - [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [74/fb002d] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (F3H-OX3-120min-28-34C-R1) [100%] 1 of 1, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [c6/42e5fc] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (F3H-OX3-120min-28-34C-R3) [100%] 3 of 3, cached: 3 [87/ece289] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (F3H-OX3-120min-28-34C-R1) [100%] 2 of 2, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [f6/16a0f4] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (F3H-OX4-120min-28-34C-R1) [100%] 7 of 7, cached: 7 [a0/95faca] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (F3H-OX3-120min-28C-R3) [100%] 6 of 6, cached: 6 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [f5/6791f0] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (F3H-OX4-120min-28C-R2) [100%] 11 of 11, cached: 11 [40/f557e4] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (F3H-OX4-120min-28C-R1) [100%] 10 of 10, cached: 10 [b5/a928cf] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28-34C-R2) [100%] 2 of 2, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [10/782590] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (VF36-120min-28-34C-R2) [100%] 14 of 14, cached: 14 [40/f557e4] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (F3H-OX4-120min-28C-R1) [100%] 10 of 10, cached: 10 [b5/a928cf] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28-34C-R2) [100%] 2 of 2, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [25/d8e378] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (VF36-120min-28C-R1) [100%] 16 of 16, cached: 16 [5c/960f14] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (VF36-120min-28-34C-R1) [100%] 13 of 13, cached: 13 [b5/a928cf] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28-34C-R2) [100%] 2 of 2, cached: 2 [7b/2ee3fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R2) [100%] 1 of 1, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d0/cfad96] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R2) [ 50%] 1 of 2, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [2f/d82aa5] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28-34C-R1) [100%] 20 of 20, cached: 20 [41/73a454] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (VF36-120min-28C-R1) [100%] 16 of 16, cached: 16 [09/3991f0] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R1) [ 80%] 4 of 5, cached: 4 [6e/f8b122] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R1) [ 75%] 3 of 4, cached: 3 [5d/ac56a6] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R2) [100%] 1 of 1, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d0/cfad96] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R2) [ 50%] 1 of 2, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [ff/ae6ad5] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (VF36-120min-28C-R2) [100%] 17 of 17, cached: 17 [43/fa5e43] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R3) [ 83%] 5 of 6, cached: 5 [6e/f8b122] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R1) [ 75%] 3 of 4, cached: 3 [5d/ac56a6] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R2) [100%] 1 of 1, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [23/86574d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R3) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP [ 0%] 0 of 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES [ 0%] 0 of 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (1) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [94/a8b3c4] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28-34C-R3) [100%] 21 of 21, cached: 21 [96/b816b8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R3) [ 70%] 7 of 10, cached: 7 [ac/de408f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R2) [ 86%] 6 of 7, cached: 6 [81/ba6356] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R3) [100%] 3 of 3, cached: 3 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 86%] 6 of 7, cached: 6 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP [ 0%] 0 of 3 [ab/5e677b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R3) [ 17%] 1 of 6, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (1) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [b4/087d69] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R2) [100%] 23 of 23, cached: 23 [82/639aa4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R3) [ 75%] 9 of 12, cached: 9 [ac/de408f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R2) [ 86%] 6 of 7, cached: 6 [81/ba6356] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R3) [100%] 3 of 3, cached: 3 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 86%] 6 of 7, cached: 6 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a8/747059] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R2) [ 33%] 2 of 6, cached: 2 [ab/5e677b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R3) [ 17%] 1 of 6, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (1) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [b4/087d69] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R2) [100%] 23 of 23, cached: 23 [82/639aa4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R3) [ 75%] 9 of 12, cached: 9 [ac/de408f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R2) [ 86%] 6 of 7, cached: 6 [81/ba6356] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R3) [100%] 3 of 3, cached: 3 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 86%] 6 of 7, cached: 6 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a8/747059] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R2) [ 33%] 2 of 6, cached: 2 [ab/5e677b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R3) [ 17%] 1 of 6, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (1) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [b4/087d69] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R2) [100%] 23 of 23, cached: 23 [82/639aa4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R3) [ 75%] 9 of 12, cached: 9 [ac/de408f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R2) [ 86%] 6 of 7, cached: 6 [81/ba6356] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R3) [100%] 3 of 3, cached: 3 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 86%] 6 of 7, cached: 6 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a8/747059] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R2) [ 33%] 2 of 6, cached: 2 [ab/5e677b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R3) [ 17%] 1 of 6, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE - [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (2) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [b4/087d69] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R2) [100%] 23 of 23, cached: 23 [82/639aa4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R3) [ 69%] 9 of 13, cached: 9 [9e/0dfe7e] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R1) [ 88%] 7 of 8, cached: 7 [81/ba6356] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R3) [100%] 3 of 3, cached: 3 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 86%] 6 of 7, cached: 6 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a8/747059] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R2) [ 33%] 2 of 6, cached: 2 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 17%] 1 of 6, cached: 1 [19/c74156] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R3) [100%] 1 of 1, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ - [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (3) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6e/bd7495] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R3) [ 73%] 11 of 15, cached: 11 [ea/c26d0d] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R1) [ 90%] 9 of 10, cached: 9 [39/91bc07] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [100%] 9 of 9, cached: 9 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [96/53ae45] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R3) [ 91%] 10 of 11, cached: 10 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a8/747059] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R2) [ 22%] 2 of 9, cached: 2 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 11%] 1 of 9, cached: 1 [19/c74156] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R3) [100%] 1 of 1, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (4) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [c1/249142] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28C-R1) [ 76%] 13 of 17, cached: 13 [fe/6c3062] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28C-R1) [ 92%] 12 of 13, cached: 12 [45/4c6537] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 92%] 11 of 12, cached: 11 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [96/53ae45] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R3) [ 91%] 10 of 11, cached: 10 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [fb/c3b048] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R2) [ 17%] 2 of 12, cached: 2 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 8%] 1 of 12, cached: 1 [19/c74156] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R3) [100%] 1 of 1, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (5) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [ 79%] 15 of 19, cached: 15 [76/24d582] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28C-R3) [ 93%] 14 of 15, cached: 14 [fa/f59e07] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R3) [ 93%] 13 of 14, cached: 13 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [64/29861b] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28-34C-R1) [ 93%] 14 of 15, cached: 14 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [9b/d2dea2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28-34C-R1) [ 29%] 4 of 14, cached: 4 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 7%] 1 of 14, cached: 1 [19/c74156] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R3) [100%] 1 of 1, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (6) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [41/fa30d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28-34C-R2) [ 77%] 17 of 22, cached: 17 [8d/f6d6f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28-34C-R3) [ 94%] 16 of 17, cached: 16 [fa/f59e07] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R3) [ 93%] 13 of 14, cached: 13 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1a/8d08d6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28-34C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [e0/bac76a] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R1) [ 29%] 4 of 14, cached: 4 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 7%] 1 of 14, cached: 1 [19/c74156] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R3) [100%] 1 of 1, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (6) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [41/fa30d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28-34C-R2) [ 77%] 17 of 22, cached: 17 [8d/f6d6f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28-34C-R3) [ 94%] 16 of 17, cached: 16 [b6/22f12a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 94%] 15 of 16, cached: 15 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1a/8d08d6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28-34C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [6a/4a749a] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28-34C-R3) [ 38%] 6 of 16, cached: 6 [20/e82ccb] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R3) [ 19%] 3 of 16, cached: 3 [19/c74156] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R3) [100%] 1 of 1, cached: 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 2 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 2 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (8) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [07/6e25ec] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R1) [ 78%] 18 of 23, cached: 18 [8d/f6d6f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28-34C-R3) [ 89%] 16 of 18, cached: 16 [b6/22f12a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 94%] 15 of 16, cached: 15 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1a/8d08d6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28-34C-R2) [ 89%] 16 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [45/b61da7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R3) [ 38%] 6 of 16, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 19%] 3 of 16, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (9) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [07/6e25ec] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R1) [ 78%] 18 of 23, cached: 18 [8d/f6d6f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28-34C-R3) [ 89%] 16 of 18, cached: 16 [b6/22f12a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 94%] 15 of 16, cached: 15 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1a/8d08d6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28-34C-R2) [ 89%] 16 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [45/b61da7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R3) [ 38%] 6 of 16, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 19%] 3 of 16, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (11) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [55/503c8b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R3) [ 79%] 19 of 24, cached: 19 [8d/f6d6f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28-34C-R3) [ 89%] 16 of 18, cached: 16 [b6/22f12a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 94%] 15 of 16, cached: 15 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1a/8d08d6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28-34C-R2) [ 89%] 16 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [45/b61da7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R3) [ 38%] 6 of 16, cached: 6 [da/bbf3ff] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R3) [ 19%] 3 of 16, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (12) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [b6/22f12a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 94%] 15 of 16, cached: 15 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [45/b61da7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R3) [ 35%] 6 of 17, cached: 6 [da/bbf3ff] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (13) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [9f/22df82] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R3) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [45/b61da7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R3) [ 35%] 6 of 17, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (15) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [9f/22df82] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R3) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [1a/a53838] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (17) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [9f/22df82] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R3) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [1a/a53838] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (18) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [9f/22df82] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R3) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [1a/a53838] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [03/3c2f87] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (19) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [9f/22df82] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R3) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [1a/a53838] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [03/3c2f87] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [20/2f8cbf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (20) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [9f/22df82] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R3) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [1a/a53838] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [03/3c2f87] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION [ 0%] 0 of 3 [20/2f8cbf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [ad/88e1f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (22) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [9f/22df82] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R3) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [1a/a53838] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [03/3c2f87] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION [ 0%] 0 of 3 [c3/d1a98b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [20/2f8cbf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [ad/88e1f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (25) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [9f/22df82] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R3) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [1a/a53838] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [03/3c2f87] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [69/20eb61] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [c3/d1a98b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [20/2f8cbf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [ad/88e1f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (29) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [9f/22df82] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R3) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [d7/3eec8e] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [b2/7a1365] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R1) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [03/3c2f87] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [69/20eb61] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [c3/d1a98b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [20/2f8cbf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [ad/88e1f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (36) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [9f/22df82] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R3) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [15/5f72f7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R1) [ 35%] 6 of 17, cached: 6 [f2/690344] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R3) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [03/3c2f87] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [69/20eb61] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [c3/d1a98b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [20/2f8cbf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [ad/88e1f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (40) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [15/5f72f7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R1) [ 35%] 6 of 17, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [03/3c2f87] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [69/20eb61] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [c3/d1a98b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [20/2f8cbf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [ad/88e1f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (44) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [15/5f72f7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R1) [ 35%] 6 of 17, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [e8/5da880] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R2) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [03/3c2f87] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [69/20eb61] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [c3/d1a98b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [ 0%] 0 of 3 [ad/88e1f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (52) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [15/5f72f7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R1) [ 35%] 6 of 17, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 0%] 0 of 3 [e8/5da880] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R2) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [ 0%] 0 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 0%] 0 of 3 [23/6170fd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R2) [ 0%] 0 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 0%] 0 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (55) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [15/5f72f7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R1) [ 35%] 6 of 17, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 0%] 0 of 3 [23/6170fd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R2) [ 0%] 0 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (58) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [15/5f72f7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R1) [ 35%] 6 of 17, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [39/779028] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R2) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 0%] 0 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [ 0%] 0 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (60) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [15/5f72f7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R1) [ 35%] 6 of 17, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 0%] 0 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [ 0%] 0 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (62) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [81/6f67be] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [d8/ef9d7e] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R3) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [15/5f72f7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R1) [ 35%] 6 of 17, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [16/b36f9f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 0%] 0 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [ 0%] 0 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [ 0%] 0 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [ 0%] 0 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [ 0%] 0 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [ 0%] 0 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [ 67%] 2 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [ 0%] 0 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - WARN: ============================================================================= Biotype attribute 'gene_biotype' not found in the last column of the GTF file! Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 Amend '--featurecounts_group_type' to change this behaviour. =================================================================================== executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 16 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [ 0%] 0 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [ 0%] 0 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [ 0%] 0 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [24/b84f32] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R3) [ 33%] 1 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 67%] 2 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 67%] 2 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 0%] 0 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 67%] 2 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 33%] 1 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 67%] 2 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [d2/6735f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 33%] 1 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 67%] 2 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [69/20eb61] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 33%] 1 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 67%] 2 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [69/20eb61] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 33%] 1 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 67%] 2 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [35/b62a25] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R3) [ 33%] 1 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 67%] 2 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [57/079a0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [25/ed0083] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R2) [ 67%] 2 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ca/1c6327] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 0%] 0 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (69) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 89%] 17 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [100%] 17 of 17, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 35%] 6 of 17, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 18%] 3 of 17, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [c3/d1a98b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 33%] 1 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (70) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [ef/169075] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [67/46809a] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 94%] 17 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 33%] 6 of 18, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 17%] 3 of 18, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [c3/d1a98b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 33%] 1 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (72) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [ef/169075] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [45/2a9c69] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 94%] 17 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 33%] 6 of 18, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [ 17%] 3 of 18, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [c3/d1a98b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 33%] 1 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (72) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [ef/169075] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [45/2a9c69] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 94%] 17 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 33%] 6 of 18, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [ 17%] 3 of 18, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/e3d10f] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 33%] 1 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (72) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [ef/169075] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [45/2a9c69] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 94%] 17 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [76/ff8dc6] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 33%] 6 of 18, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [ 17%] 3 of 18, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ad/3567c4] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R3) [ 67%] 2 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 33%] 1 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (72) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [ef/169075] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [45/2a9c69] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 94%] 17 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 33%] 6 of 18, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [ 17%] 3 of 18, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ad/3567c4] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R3) [ 67%] 2 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [20/f518df] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R3) [ 33%] 1 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (72) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [ef/169075] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [45/2a9c69] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 94%] 17 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 33%] 6 of 18, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [ 17%] 3 of 18, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ad/3567c4] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R3) [ 67%] 2 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [20/2f8cbf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (72) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [ef/169075] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [45/2a9c69] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 94%] 17 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 33%] 6 of 18, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [ 17%] 3 of 18, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ad/3567c4] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R3) [ 67%] 2 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (72) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [ef/169075] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [45/2a9c69] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 18 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 33%] 6 of 18, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [ 17%] 3 of 18, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ad/3567c4] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R3) [ 67%] 2 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (72) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [ef/169075] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [45/2a9c69] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 18 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 33%] 6 of 18, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [ 17%] 3 of 18, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (72) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [ef/169075] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19, cached: 17 [45/2a9c69] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 18 of 18, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 33%] 6 of 18, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [ 17%] 3 of 18, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (74) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (75) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (75) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [54/c76022] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (75) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [16/b36f9f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R3) [ 33%] 1 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP - [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [ad/88e1f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (77) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [16/b36f9f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R3) [ 33%] 1 of 3 [08/10f6e6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R3) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG - [29/1c9e89] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R3) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG - [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [ad/88e1f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (78) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [16/b36f9f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R3) [ 33%] 1 of 3 [08/10f6e6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R3) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG [ 0%] 0 of 1 [29/1c9e89] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R3) [100%] 1 of 1 [04/19338d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [ 0%] 0 of 1 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (79) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [16/b36f9f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R3) [ 33%] 1 of 3 [08/10f6e6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R3) [100%] 1 of 1 [af/daccb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [ 0%] 0 of 1 [29/1c9e89] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R3) [100%] 1 of 1 [04/19338d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [ 0%] 0 of 1 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (79) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [16/b36f9f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R3) [ 33%] 1 of 3 [08/10f6e6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R3) [100%] 1 of 1 [af/daccb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [ 0%] 0 of 1 [29/1c9e89] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R3) [100%] 1 of 1 [04/19338d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [ 0%] 0 of 1 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (79) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [16/b36f9f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R3) [ 33%] 1 of 3 [08/10f6e6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R3) [100%] 1 of 1 [af/daccb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [ 0%] 0 of 1 [29/1c9e89] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R3) [100%] 1 of 1 [04/19338d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [100%] 1 of 1 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (79) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [16/b36f9f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R3) [ 33%] 1 of 3 [08/10f6e6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R3) [100%] 1 of 1 [af/daccb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [100%] 1 of 1 [29/1c9e89] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R3) [100%] 1 of 1 [04/19338d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [100%] 1 of 1 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (79) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [08/10f6e6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R3) [ 50%] 1 of 2 [af/daccb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [100%] 1 of 1 [29/1c9e89] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R3) [ 50%] 1 of 2 [04/19338d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [100%] 1 of 1 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (81) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [61/efdbdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R3) [ 50%] 1 of 2 [af/daccb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [100%] 1 of 1 [62/cad20b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R3) [ 50%] 1 of 2 [04/19338d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R3) [100%] 1 of 1 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (83) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [61/efdbdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [1e/0deb8d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [ 50%] 1 of 2 [62/cad20b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [a6/3f0414] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [ 50%] 1 of 2 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (83) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [61/efdbdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [1e/0deb8d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [ 50%] 1 of 2 [62/cad20b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [a6/3f0414] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [ 50%] 1 of 2 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (83) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [61/efdbdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [1e/0deb8d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [62/cad20b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [a6/3f0414] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [ 50%] 1 of 2 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (83) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [61/b66258] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [61/efdbdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [1e/0deb8d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [62/cad20b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [a6/3f0414] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 0%] 0 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (85) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 67%] 2 of 3 [1e/0deb8d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 67%] 2 of 3 [a6/3f0414] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (85) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 67%] 2 of 3 [1e/0deb8d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [100%] 2 of 2 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [a6/3f0414] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 32%] 6 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [ 67%] 2 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [ 67%] 2 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [e0/bac76a] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R1) [ 37%] 7 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [ 67%] 2 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [ 67%] 2 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [bd/a80453] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28C-R1) [ 42%] 8 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [ 67%] 2 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [ 67%] 2 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [1a/a53838] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R3) [ 47%] 9 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [ 67%] 2 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [1a/a53838] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R3) [ 47%] 9 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [d7/3eec8e] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28C-R3) [ 53%] 10 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [45/b61da7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R3) [ 63%] 12 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [15/5f72f7] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R1) [ 74%] 14 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [9e/74de72] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R1) [ 79%] 15 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [ef/ba91f9] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [b6/d03a1a] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R3) [ 33%] 1 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [ef/ba91f9] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 89%] 17 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [e4/69e035] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R3) [ 67%] 2 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [2f/ab7a4b] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R3) [ 89%] 17 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [e8/5da880] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R2) [100%] 3 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [aa/3361fe] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R1) [ 95%] 18 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [e8/5da880] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R2) [100%] 3 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 16%] 3 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [100%] 3 of 3, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [e8/5da880] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R2) [100%] 3 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (87) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [4d/762279] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R2) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [100%] 3 of 3 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 3 [e8/5da880] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R2) [100%] 3 of 3 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [100%] 3 of 3 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [100%] 3 of 3 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [100%] 3 of 3 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [100%] 3 of 3 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [100%] 3 of 3 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [100%] 3 of 3 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [100%] 3 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (88) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [40/0ee4d5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R3) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 4 [e8/5da880] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R2) [ 75%] 3 of 4 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [ 75%] 3 of 4 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [ 75%] 3 of 4 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [ 75%] 3 of 4 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [ 75%] 3 of 4 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (89) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 0%] 0 of 4 [e8/5da880] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R2) [ 75%] 3 of 4 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [ 75%] 3 of 4 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [ 75%] 3 of 4 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [ 75%] 3 of 4 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [ 75%] 3 of 4 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (91) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 4 [e8/5da880] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R2) [ 75%] 3 of 4 [5c/758359] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R2) [ 75%] 3 of 4 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [ 75%] 3 of 4 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [ 75%] 3 of 4 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [ 75%] 3 of 4 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (92) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 4 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 75%] 3 of 4 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 75%] 3 of 4 [b3/9880b1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R3) [ 75%] 3 of 4 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [ 75%] 3 of 4 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [ 75%] 3 of 4 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (93) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 4 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 75%] 3 of 4 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 75%] 3 of 4 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 75%] 3 of 4 [ce/ef87f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R3) [ 75%] 3 of 4 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [ 75%] 3 of 4 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (94) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 4 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 75%] 3 of 4 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 75%] 3 of 4 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 75%] 3 of 4 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 75%] 3 of 4 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [46/2e7c2b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R2) [ 75%] 3 of 4 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (96) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 4 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 75%] 3 of 4 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 75%] 3 of 4 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 75%] 3 of 4 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 75%] 3 of 4 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [ef/8c7603] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 75%] 3 of 4 [31/94d361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (97) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [a5/eacdc2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R2) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 4 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 75%] 3 of 4 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 75%] 3 of 4 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 75%] 3 of 4 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 75%] 3 of 4 [1a/ee3492] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R2) [ 75%] 3 of 4 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 75%] 3 of 4 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (99) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 4 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 75%] 3 of 4 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 75%] 3 of 4 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 75%] 3 of 4 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 75%] 3 of 4 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 75%] 3 of 4 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (99) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 4 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 75%] 3 of 4 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 75%] 3 of 4 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 75%] 3 of 4 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 75%] 3 of 4 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 75%] 3 of 4 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (99) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [fb/dc9294] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28-34C-R1) [ 21%] 4 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 4 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 75%] 3 of 4 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 75%] 3 of 4 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 75%] 3 of 4 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [100%] 4 of 4 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 75%] 3 of 4 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (99) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b2/7a1365] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R1) [ 26%] 5 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 75%] 3 of 4, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 75%] 3 of 4 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 4 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 75%] 3 of 4 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 75%] 3 of 4 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 75%] 3 of 4 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [100%] 4 of 4 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 60%] 3 of 5 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 75%] 3 of 4 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (101) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b2/7a1365] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R1) [ 26%] 5 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 60%] 3 of 5 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 60%] 3 of 5 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 6 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 50%] 3 of 6 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 50%] 3 of 6 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 50%] 3 of 6 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 60%] 3 of 5 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 60%] 3 of 5 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 75%] 3 of 4 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (103) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [4b/4c271e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 6 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 50%] 3 of 6 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 50%] 3 of 6 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 50%] 3 of 6 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (104) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 0%] 0 of 6 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 50%] 3 of 6 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 50%] 3 of 6 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 50%] 3 of 6 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (106) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 50%] 3 of 6 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 50%] 3 of 6 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 50%] 3 of 6 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (107) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [40/3a67bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 50%] 3 of 6 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 50%] 3 of 6 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (108) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 50%] 3 of 6 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 50%] 3 of 6 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (110) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 50%] 3 of 6 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (111) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [0d/24e387] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [d1/d96db9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28-34C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (113) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [20/e39f34] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R3) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (114) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [14/60c310] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28-34C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (115) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [d7/b0c3da] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (117) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [79/51c9e3] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [e9/2d4d98] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (118) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 67%] 4 of 6 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [e9/2d4d98] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (121) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 67%] 4 of 6 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [e9/2d4d98] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (123) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e4/0e9be7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R3) [ 32%] 6 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [37/1ab9d1] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d9/fa62b8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 67%] 4 of 6 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [e9/2d4d98] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (123) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [37/1ab9d1] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d9/fa62b8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 0%] 0 of 6 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 67%] 4 of 6 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [e9/2d4d98] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 50%] 3 of 6 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (125) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [26/41c48c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d9/fa62b8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [67/9a5b96] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R3) [ 14%] 1 of 7 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 57%] 4 of 7 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [e9/2d4d98] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (126) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [26/41c48c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d9/fa62b8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 57%] 4 of 7 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [e9/2d4d98] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (127) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 57%] 4 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d9/fa62b8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 57%] 4 of 7 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [e9/2d4d98] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (129) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 57%] 4 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d9/fa62b8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 57%] 4 of 7 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [e9/2d4d98] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (130) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 57%] 4 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d9/fa62b8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 57%] 4 of 7 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [e9/2d4d98] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (131) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 57%] 4 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d9/fa62b8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 57%] 4 of 7 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (133) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 57%] 4 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d9/fa62b8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 57%] 4 of 7 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (134) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 57%] 4 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d9/fa62b8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R3) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 57%] 4 of 7 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (135) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 57%] 4 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 57%] 4 of 7 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (135) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 57%] 4 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 57%] 4 of 7 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (135) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 57%] 4 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 57%] 4 of 7 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (135) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [4f/54b1d8] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 57%] 4 of 7, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 14%] 1 of 7 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 57%] 4 of 7 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (136) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 50%] 4 of 8, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 13%] 1 of 8 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [20/e39f34] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R3) [ 63%] 5 of 8 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (138) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 50%] 4 of 8, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 13%] 1 of 8 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [20/d47a95] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R1) [ 75%] 6 of 8 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (139) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 50%] 4 of 8, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 13%] 1 of 8 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [88/c40921] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R2) [ 75%] 6 of 8 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (140) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 50%] 4 of 8, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 13%] 1 of 8 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [88/c40921] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R2) [ 75%] 6 of 8 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (141) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 50%] 4 of 8, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 13%] 1 of 8 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [88/c40921] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R2) [ 75%] 6 of 8 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [3a/9d215e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (143) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 50%] 4 of 8, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 13%] 1 of 8 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [88/c40921] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R2) [ 75%] 6 of 8 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [3a/9d215e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (144) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19, cached: 3 [38/5849e7] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28-34C-R1) [ 50%] 4 of 8, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 13%] 1 of 8 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [88/c40921] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R2) [ 75%] 6 of 8 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [3a/9d215e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (145) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19, cached: 3 [83/96d96d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R2) [ 50%] 4 of 8, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 13%] 1 of 8 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [88/c40921] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R2) [ 75%] 6 of 8 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [3a/9d215e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (146) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19, cached: 3 [83/96d96d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R2) [ 50%] 4 of 8, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 13%] 1 of 8 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [88/c40921] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R2) [ 75%] 6 of 8 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [3a/9d215e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (147) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [39/8df881] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19, cached: 3 [83/96d96d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R2) [ 50%] 4 of 8, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 13%] 1 of 8 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [88/c40921] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R2) [ 75%] 6 of 8 [46/90cb9d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [3a/9d215e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (147) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19, cached: 3 [83/96d96d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R2) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 11%] 1 of 9 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [88/c40921] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R2) [ 67%] 6 of 9 [46/90cb9d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [3a/9d215e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (148) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19, cached: 3 [83/96d96d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R2) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 11%] 1 of 9 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [46/90cb9d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (150) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 11%] 1 of 9 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [46/90cb9d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (152) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 11%] 1 of 9 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (153) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 11%] 1 of 9 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (155) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 11%] 1 of 9 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [88/b93d55] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (157) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 11%] 1 of 9 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [88/b93d55] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (158) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 11%] 1 of 9 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [7a/12dfc1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [88/b93d55] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (159) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 11%] 1 of 9 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [1a/cf2725] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R1) [ 78%] 7 of 9 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [88/b93d55] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (159) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [b7/526bb3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 11%] 1 of 9 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [1a/cf2725] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R1) [ 78%] 7 of 9 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [88/b93d55] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (159) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [f2/690344] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R3) [ 53%] 10 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 44%] 4 of 9, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 30%] 3 of 10 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 30%] 3 of 10 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 11%] 1 of 9 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [1a/cf2725] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R1) [ 78%] 7 of 9 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 30%] 3 of 10 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 30%] 3 of 10 [88/b93d55] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R1) [ 30%] 3 of 10 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (160) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 9%] 1 of 11 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [1a/cf2725] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R1) [ 64%] 7 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [88/b93d55] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (161) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 9%] 1 of 11 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [1a/cf2725] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R1) [ 64%] 7 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [88/b93d55] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (163) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 9%] 1 of 11 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [1a/cf2725] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R1) [ 64%] 7 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [ff/0c1978] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (164) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 9%] 1 of 11 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [88/c40921] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R2) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [43/efb396] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ff/0c1978] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (165) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 9%] 1 of 11 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [82/a0ae3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R3) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [43/efb396] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ff/0c1978] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (167) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 9%] 1 of 11 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [82/a0ae3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R3) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (168) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 9%] 1 of 11 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (170) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 9%] 1 of 11 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (171) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 9%] 1 of 11 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 27%] 3 of 11 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (173) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 9%] 1 of 11 [dc/7841ae] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R3) [ 27%] 3 of 11 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (175) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [86/cb8c53] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R3) [ 9%] 1 of 11 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (176) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 9%] 1 of 11 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (177) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [46/c35032] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R3) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 9%] 1 of 11 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (178) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8c/f1c29d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R3) [ 58%] 11 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 36%] 4 of 11, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 9%] 1 of 11 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 73%] 8 of 11 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 27%] 3 of 11 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (179) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [a5/24a2b6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R1) [ 63%] 12 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 33%] 4 of 12, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 27%] 3 of 11 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 12 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 67%] 8 of 12 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 25%] 3 of 12 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 25%] 3 of 12 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 27%] 3 of 11 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (179) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [a5/24a2b6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R1) [ 63%] 12 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 33%] 4 of 12, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 12 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 67%] 8 of 12 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 25%] 3 of 12 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 25%] 3 of 12 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (180) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [a5/24a2b6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R1) [ 63%] 12 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 33%] 4 of 12, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 25%] 3 of 12 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 12 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 67%] 8 of 12 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 25%] 3 of 12 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 25%] 3 of 12 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (180) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [aa/d1abf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R1) [ 68%] 13 of 19, cached: 3 [4b/4c271e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R1) [ 42%] 5 of 12, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 25%] 3 of 12 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 12 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 67%] 8 of 12 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 25%] 3 of 12 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 25%] 3 of 12 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (181) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [aa/d1abf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R1) [ 68%] 13 of 19, cached: 3 [4b/4c271e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R1) [ 42%] 5 of 12, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 23%] 3 of 13 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 12 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 67%] 8 of 12 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 25%] 3 of 12 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 23%] 3 of 13 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (182) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [aa/d1abf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R1) [ 68%] 13 of 19, cached: 3 [4b/4c271e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R1) [ 38%] 5 of 13, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 23%] 3 of 13 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 12 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 25%] 3 of 12 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 62%] 8 of 13 [a5/e77101] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 23%] 3 of 13 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 25%] 3 of 12 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (182) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [aa/d1abf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R1) [ 68%] 13 of 19, cached: 3 [4b/4c271e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R1) [ 38%] 5 of 13, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 23%] 3 of 13 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 12 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 62%] 8 of 13 [a5/e77101] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 23%] 3 of 13 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (182) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [aa/d1abf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R1) [ 68%] 13 of 19, cached: 3 [3c/bccb40] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R3) [ 46%] 6 of 13, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 23%] 3 of 13 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 13 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 62%] 8 of 13 [a5/e77101] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 23%] 3 of 13 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (183) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [aa/d1abf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R1) [ 68%] 13 of 19, cached: 3 [26/41c48c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R2) [ 54%] 7 of 13, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 23%] 3 of 13 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 13 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 62%] 8 of 13 [f2/045168] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 23%] 3 of 13 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (184) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [aa/d1abf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R1) [ 68%] 13 of 19, cached: 3 [26/41c48c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R2) [ 54%] 7 of 13, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 23%] 3 of 13 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 13 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [c2/7abe0b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28-34C-R1) [ 31%] 4 of 13 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 62%] 8 of 13 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 23%] 3 of 13 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 23%] 3 of 13 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (185) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [aa/d1abf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R1) [ 68%] 13 of 19, cached: 3 [26/41c48c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R2) [ 54%] 7 of 13, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 23%] 3 of 13 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 8%] 1 of 13 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 23%] 3 of 13 [9d/3a6206] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R1) [ 31%] 4 of 13 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 62%] 8 of 13 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 23%] 3 of 13 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 23%] 3 of 13 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 23%] 3 of 13 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (185) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [da/bbf3ff] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19, cached: 3 [26/41c48c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R2) [ 50%] 7 of 14, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 21%] 3 of 14 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 21%] 3 of 14 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 7%] 1 of 14 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 21%] 3 of 14 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 21%] 3 of 14 [9d/3a6206] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R1) [ 29%] 4 of 14 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 57%] 8 of 14 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 21%] 3 of 14 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 21%] 3 of 14 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 21%] 3 of 14 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 21%] 3 of 14 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (185) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [26/41c48c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R2) [ 47%] 7 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 7%] 1 of 15 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [9d/3a6206] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R1) [ 27%] 4 of 15 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 53%] 8 of 15 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (186) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 47%] 7 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 7%] 1 of 15 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [9d/3a6206] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R1) [ 27%] 4 of 15 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 53%] 8 of 15 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (186) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 47%] 7 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 7%] 1 of 15 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [9d/3a6206] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R1) [ 27%] 4 of 15 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 53%] 8 of 15 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (186) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 47%] 7 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 7%] 1 of 15 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [0d/24e387] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R3) [ 33%] 5 of 15 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 53%] 8 of 15 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (188) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 47%] 7 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 7%] 1 of 15 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [0d/24e387] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R3) [ 33%] 5 of 15 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 53%] 8 of 15 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (188) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 47%] 7 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 7%] 1 of 15 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [c8/6ed95d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R1) [ 40%] 6 of 15 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 53%] 8 of 15 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (189) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 47%] 7 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 7%] 1 of 15 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 47%] 7 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (191) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 60%] 9 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 47%] 7 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (192) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 60%] 9 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [eb/617d97] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R2) [ 47%] 7 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (192) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 60%] 9 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 20%] 3 of 15 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 53%] 8 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (193) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 60%] 9 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 53%] 8 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 27%] 4 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (193) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 60%] 9 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 53%] 8 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 27%] 4 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (194) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [25/445f0e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R1) [ 60%] 9 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 53%] 8 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 27%] 4 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (194) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [46/c35032] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R3) [ 67%] 10 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 53%] 8 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 27%] 4 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (195) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [46/c35032] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R3) [ 67%] 10 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d7/f48f98] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 53%] 8 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 27%] 4 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (196) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [46/c35032] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R3) [ 67%] 10 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 27%] 4 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 27%] 4 of 15 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 53%] 8 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 27%] 4 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (196) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 73%] 11 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [24/4f1897] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28-34C-R1) [ 27%] 4 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 27%] 4 of 15 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 53%] 8 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 27%] 4 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (197) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [88/b36552] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 73%] 11 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 27%] 4 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 7%] 1 of 15 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 27%] 4 of 15 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 53%] 8 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 27%] 4 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (198) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 73%] 11 of 15, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 27%] 4 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 20%] 3 of 15 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 27%] 4 of 15 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 53%] 8 of 15 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 53%] 8 of 15 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 27%] 4 of 15 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 20%] 3 of 15 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 20%] 3 of 15 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (198) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 69%] 11 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 50%] 8 of 16 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 50%] 8 of 16 [7e/955e80] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28-34C-R1) [ 25%] 4 of 16 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (199) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 69%] 11 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 50%] 8 of 16 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 50%] 8 of 16 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 25%] 4 of 16 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (199) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 69%] 11 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 50%] 8 of 16 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 50%] 8 of 16 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 31%] 5 of 16 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (199) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [fa/8f33ea] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R3) [ 69%] 11 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 50%] 8 of 16 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 50%] 8 of 16 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 31%] 5 of 16 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (200) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 69%] 11 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 50%] 8 of 16 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 50%] 8 of 16 [86/568209] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R2) [ 31%] 5 of 16 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (200) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 69%] 11 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [be/2221c0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R2) [ 50%] 8 of 16 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 50%] 8 of 16 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 38%] 6 of 16 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (201) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 69%] 11 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 50%] 8 of 16 [c9/b69ff4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R3) [ 38%] 6 of 16 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (201) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 69%] 11 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 50%] 8 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (202) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 69%] 11 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (203) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 69%] 11 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (203) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 75%] 12 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (203) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 75%] 12 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 19%] 3 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (204) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 75%] 12 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [80/f78f9e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28-34C-R1) [ 25%] 4 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 25%] 4 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (205) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 75%] 12 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 25%] 4 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 19%] 3 of 16 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 31%] 5 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 25%] 4 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (206) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 75%] 12 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 31%] 5 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 6%] 1 of 16 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 19%] 3 of 16 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 31%] 5 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 25%] 4 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (207) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 75%] 12 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 31%] 5 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 16 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 19%] 3 of 16 [65/c3c4e9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R2) [ 31%] 5 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 25%] 4 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (207) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [f8/d42515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R1) [ 75%] 12 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0f/0f98de] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R1) [ 31%] 5 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 16 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 19%] 3 of 16 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 25%] 4 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (209) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 75%] 12 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [37/1ab9d1] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R3) [ 38%] 6 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 16 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 19%] 3 of 16 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 25%] 4 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (210) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 75%] 12 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 44%] 7 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 16 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 19%] 3 of 16 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 25%] 4 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (211) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 75%] 12 of 16, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 44%] 7 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 19%] 3 of 16 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 16 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 19%] 3 of 16 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 50%] 8 of 16 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 56%] 9 of 16 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 25%] 4 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 19%] 3 of 16 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (211) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [9f/6d6515] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 71%] 12 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 17 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 19%] 3 of 16 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 44%] 7 of 16 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 47%] 8 of 17 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 53%] 9 of 17 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 25%] 4 of 16 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 18%] 3 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 19%] 3 of 16 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (212) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 71%] 12 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 17 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 18%] 3 of 17 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 47%] 8 of 17 [82/a0ae3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R3) [ 59%] 10 of 17 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 24%] 4 of 17 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 18%] 3 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (212) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 71%] 12 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 17 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 18%] 3 of 17 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 47%] 8 of 17 [82/a0ae3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R3) [ 59%] 10 of 17 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 24%] 4 of 17 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 18%] 3 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (212) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 71%] 12 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 17 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 18%] 3 of 17 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 47%] 8 of 17 [82/a0ae3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R3) [ 59%] 10 of 17 [77/7cd58b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 24%] 4 of 17 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 18%] 3 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (213) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 71%] 12 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a9/6aabcd] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 17 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 18%] 3 of 17 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 47%] 8 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 41%] 7 of 17 [34/746faa] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28-34C-R1) [ 24%] 4 of 17 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 18%] 3 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (216) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 71%] 12 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 41%] 7 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 17 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 18%] 3 of 17 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 47%] 8 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 41%] 7 of 17 [79/51c9e3] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R3) [ 29%] 5 of 17 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 24%] 4 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (217) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 71%] 12 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 47%] 8 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 41%] 7 of 17 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 35%] 6 of 17 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 24%] 4 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (217) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 71%] 12 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [d6/5f12ad] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R1) [ 41%] 7 of 17 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 47%] 8 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 41%] 7 of 17 [39/0ff93a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R1) [ 35%] 6 of 17 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 24%] 4 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (219) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 71%] 12 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [21/293cbb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R3) [ 41%] 7 of 17 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 41%] 7 of 17 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 24%] 4 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (219) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 71%] 12 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [21/293cbb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R3) [ 41%] 7 of 17 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 41%] 7 of 17 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 24%] 4 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (220) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 76%] 13 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 41%] 7 of 17 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 41%] 7 of 17 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 24%] 4 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (221) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 76%] 13 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 41%] 7 of 17 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [46/90cb9d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 24%] 4 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (221) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 76%] 13 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 41%] 7 of 17 [1f/831228] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [46/90cb9d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 24%] 4 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (222) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 76%] 13 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [46/90cb9d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [29/7c242e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 24%] 4 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (224) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 76%] 13 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [46/90cb9d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [d7/b0c3da] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R3) [ 29%] 5 of 17 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (225) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 76%] 13 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [d7/b0c3da] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R3) [ 29%] 5 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (225) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 76%] 13 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2f/362678] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [d7/b0c3da] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R3) [ 29%] 5 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (227) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [a3/36c5fc] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R1) [ 76%] 13 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e0/3ccec3] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R3) [ 47%] 8 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0f/b338f2] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (228) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [a1/214790] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R3) [ 76%] 13 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0f/b338f2] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 53%] 9 of 17 [70/f14d67] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R3) [ 65%] 11 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (229) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [a1/214790] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R3) [ 76%] 13 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0f/b338f2] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 53%] 9 of 17 [74/9ffe28] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R1) [ 71%] 12 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (230) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0f/b338f2] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R3) [ 6%] 1 of 17 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 53%] 9 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (231) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0f/b338f2] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R3) [ 6%] 1 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 53%] 9 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (231) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0f/b338f2] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R3) [ 6%] 1 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [8e/556416] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R3) [ 59%] 10 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (232) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 6%] 1 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [8e/556416] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R3) [ 59%] 10 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (232) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 6%] 1 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 65%] 11 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (232) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e2/9f9b40] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 6%] 1 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 65%] 11 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [53/88d42c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R2) [ 41%] 7 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (234) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 6%] 1 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [9c/ff4727] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 65%] 11 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [69/f353ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [3a/9d215e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R2) [ 47%] 8 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (235) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 6%] 1 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 65%] 11 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [07/c65b63] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R2) [ 47%] 8 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (235) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [cd/922c0b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 6%] 1 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 65%] 11 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [76/908b9b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [07/c65b63] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R2) [ 47%] 8 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (237) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 6%] 1 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [19/192016] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R3) [ 65%] 11 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (237) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 6%] 1 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [9d/3a6206] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R1) [ 71%] 12 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (238) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 12%] 2 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 71%] 12 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (239) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 12%] 2 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [8a/f20bf7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R2) [ 71%] 12 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (239) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 12%] 2 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 76%] 13 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [99/be9eeb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (240) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 53%] 9 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 12%] 2 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 76%] 13 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [6d/0f519f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28-34C-R1) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (241) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 59%] 10 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 12%] 2 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 76%] 13 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (241) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 59%] 10 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 12%] 2 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [c0/8704f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 76%] 13 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (242) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 59%] 10 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 12%] 2 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 59%] 10 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 76%] 13 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (242) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 59%] 10 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 12%] 2 of 17 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 18%] 3 of 17 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 59%] 10 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 76%] 13 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (243) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 59%] 10 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 12%] 2 of 17 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 18%] 3 of 17 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 59%] 10 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 76%] 13 of 17 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (243) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 59%] 10 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [0c/c4129d] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R2) [ 12%] 2 of 17 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 18%] 3 of 17 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 59%] 10 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [5b/f6c4cc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R1) [ 76%] 13 of 17 [a5/e77101] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R3) [ 59%] 10 of 17 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (244) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/9433a5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R3) [ 59%] 10 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [6f/744e35] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R3) [ 12%] 2 of 17 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 18%] 3 of 17 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 59%] 10 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17 [a5/e77101] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R3) [ 59%] 10 of 17 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 53%] 9 of 17 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (246) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [8e/da5c2d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R3) [ 89%] 17 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 82%] 14 of 17, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 59%] 10 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 18%] 3 of 17 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 18%] 3 of 17 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 18%] 3 of 17 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 59%] 10 of 17 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 71%] 12 of 17 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 82%] 14 of 17 [a5/e77101] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R3) [ 59%] 10 of 17 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 53%] 9 of 17 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 24%] 4 of 17 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (246) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 56%] 10 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 17%] 3 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 56%] 10 of 18 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 67%] 12 of 18 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [a5/e77101] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [01/bf22e7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R1) [ 50%] 9 of 18 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 22%] 4 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (247) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 56%] 10 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 17%] 3 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 56%] 10 of 18 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 67%] 12 of 18 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [a5/e77101] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 22%] 4 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (247) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 56%] 10 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 17%] 3 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 56%] 10 of 18 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 67%] 12 of 18 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [a5/e77101] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 28%] 5 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (248) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 56%] 10 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 17%] 3 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [b3/2fcee4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R3) [ 56%] 10 of 18 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 67%] 12 of 18 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 28%] 5 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (248) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 56%] 10 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 17%] 3 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 67%] 12 of 18 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 28%] 5 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (249) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 56%] 10 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 17%] 3 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 67%] 12 of 18 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [75/5a12e5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R2) [ 28%] 5 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (249) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 56%] 10 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 17%] 3 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 67%] 12 of 18 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 33%] 6 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (249) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 56%] 10 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 17%] 3 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [100%] 3 of 3 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 67%] 12 of 18 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 33%] 6 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (250) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 56%] 10 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [46/32b164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R3) [ 67%] 12 of 18 [76/244ff2] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 33%] 6 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (251) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 56%] 10 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [46/32b164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R3) [ 67%] 12 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 33%] 6 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (251) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 61%] 11 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [46/32b164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R3) [ 67%] 12 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 56%] 10 of 18 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 33%] 6 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (252) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 61%] 11 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [46/32b164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R3) [ 67%] 12 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 56%] 10 of 18 [00/e9ec0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R3) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 33%] 6 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (252) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 61%] 11 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 17%] 3 of 18 [a0/ba631d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [46/32b164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R3) [ 67%] 12 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [f2/045168] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [00/e9ec0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R3) [ 50%] 9 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [86/17bdb9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R1) [ 33%] 6 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (255) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 61%] 11 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [cf/b42a11] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R3) [ 17%] 3 of 18 [36/498fec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R3) [ 61%] 11 of 18 [46/32b164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R3) [ 67%] 12 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [f2/045168] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [43/efb396] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R3) [ 56%] 10 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 39%] 7 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (255) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 61%] 11 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [cf/b42a11] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R3) [ 17%] 3 of 18 [36/498fec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R3) [ 61%] 11 of 18 [46/32b164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R3) [ 67%] 12 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [f2/045168] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [76/2a4858] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R3) [ 61%] 11 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 39%] 7 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (256) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 61%] 11 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [cf/b42a11] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R3) [ 17%] 3 of 18 [36/498fec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R3) [ 61%] 11 of 18 [46/32b164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R3) [ 67%] 12 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [f2/045168] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R3) [ 61%] 11 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 39%] 7 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (257) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 61%] 11 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [cf/b42a11] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R3) [ 17%] 3 of 18 [36/498fec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R3) [ 61%] 11 of 18 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 72%] 13 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [19/643e12] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R1) [ 39%] 7 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (258) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 61%] 11 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [cf/b42a11] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R3) [ 17%] 3 of 18 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 61%] 11 of 18 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 72%] 13 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (259) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [a3/8651d7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R3) [ 61%] 11 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 61%] 11 of 18 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 72%] 13 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (259) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 61%] 11 of 18 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 72%] 13 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (259) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [98/fa9ae0] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R3) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 61%] 11 of 18 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 72%] 13 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (260) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 79%] 19 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [100%] 19 of 19, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [31/820711] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28-34C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 61%] 11 of 18 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 72%] 13 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 50%] 9 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (261) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [b4/01ef50] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R1) [ 22%] 4 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 75%] 3 of 4 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 61%] 11 of 18 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 72%] 13 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 56%] 10 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (261) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [fb/e33ca7] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [0d/ff1f89] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R1) [ 28%] 5 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 60%] 3 of 5 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 60%] 3 of 5 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 61%] 11 of 18 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 72%] 13 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [a6/d39b1b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [89/a08e3e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R3) [ 56%] 10 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (264) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 39%] 7 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 61%] 11 of 18 [8f/953194] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R1) [ 72%] 13 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 56%] 10 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (266) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 39%] 7 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 72%] 13 of 18 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 78%] 14 of 18 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 61%] 11 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (267) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 39%] 7 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [2e/2f50c6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R1) [ 78%] 14 of 18 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 61%] 11 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (267) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 39%] 7 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [2e/2f50c6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R1) [ 78%] 14 of 18 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 61%] 11 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (267) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 39%] 7 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [b3/c10b39] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 83%] 15 of 18 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 61%] 11 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (268) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [26/cae7a3] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 39%] 7 of 18 [26/51a2d5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R2) [ 43%] 3 of 7 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [fd/9d87d8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 43%] 3 of 7 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 83%] 15 of 18 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 67%] 12 of 18 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 61%] 11 of 18 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 61%] 11 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (270) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 39%] 7 of 18 [24/d0d6f0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 43%] 3 of 7 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [fd/9d87d8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 43%] 3 of 7 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 83%] 15 of 18 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 67%] 12 of 18 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 61%] 11 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (270) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [11/31ce05] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R1) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [99/1ab8cd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R1) [ 95%] 18 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 67%] 12 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 39%] 7 of 18 [24/d0d6f0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 43%] 3 of 7 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [fd/9d87d8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 43%] 3 of 7 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 17%] 3 of 18 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 17%] 3 of 18 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 83%] 15 of 18 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 72%] 13 of 18 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 67%] 12 of 18 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 61%] 11 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 44%] 8 of 18 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (271) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 78%] 14 of 18, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [ef/e6d0fc] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R2) [ 37%] 7 of 19 [24/d0d6f0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 43%] 3 of 7 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [fd/9d87d8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 43%] 3 of 7 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 78%] 14 of 18 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 72%] 13 of 18 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 61%] 11 of 18 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (272) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 74%] 14 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [24/d0d6f0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [7b/e0ead1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R1) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (273) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 74%] 14 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [5d/26e8ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R1) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [7b/e0ead1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R1) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [f3/8a17f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (273) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 74%] 14 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [5d/26e8ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R1) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [7b/e0ead1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R1) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [8a/f20bf7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R2) [ 84%] 16 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (274) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 74%] 14 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [5d/26e8ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R1) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c3/106c9d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R3) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [8a/f20bf7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R2) [ 84%] 16 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (274) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [62/e195aa] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 74%] 14 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [5d/26e8ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R1) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c3/106c9d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R3) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [8a/f20bf7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R2) [ 84%] 16 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (275) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 74%] 14 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [5e/e6f762] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R3) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c3/106c9d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R3) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [8a/f20bf7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R2) [ 84%] 16 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (275) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 74%] 14 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [5e/e6f762] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R3) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [c3/106c9d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R3) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [a6/18b311] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [8a/f20bf7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R2) [ 84%] 16 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (276) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 74%] 14 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [5e/e6f762] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R3) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [8a/f20bf7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R2) [ 84%] 16 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (276) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a1/214790] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [5e/e6f762] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R3) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [8a/f20bf7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R2) [ 84%] 16 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (277) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a1/214790] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [8a/f20bf7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28C-R2) [ 84%] 16 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [9a/519361] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [9e/0d7bb0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (279) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [1c/e1ffe7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [ 84%] 16 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [43/e9e47c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R3) [ 58%] 11 of 19 [88/b93d55] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (281) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cf/298cb5] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R2) [ 42%] 8 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 16%] 3 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (282) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (283) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [f0/ad78db] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28C-R2) [ 84%] 16 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [35/b9fddb] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R1) [ 47%] 9 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [4a/fd3164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R1) [ 68%] 13 of 19 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (284) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 89%] 17 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ac/997895] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [4a/fd3164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R1) [ 68%] 13 of 19 [4f/39f3ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (285) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 89%] 17 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [4a/fd3164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R1) [ 68%] 13 of 19 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 84%] 16 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [fd/a2ed6f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [17/71c613] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (287) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a4/48aca6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R3) [ 89%] 17 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [4a/fd3164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R1) [ 68%] 13 of 19 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 84%] 16 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (290) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [f8/626c21] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [71/6dc409] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [4a/fd3164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R1) [ 68%] 13 of 19 [3a/508d52] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28C-R2) [ 84%] 16 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (290) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [f8/626c21] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [71/6dc409] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [4a/fd3164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R1) [ 68%] 13 of 19 [46/32b164] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R3) [ 89%] 17 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 63%] 12 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (292) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [f8/626c21] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [71/6dc409] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [21/293cbb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (293) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [f8/626c21] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [71/6dc409] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [21/293cbb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (294) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [f8/626c21] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [21/293cbb] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [87/a2e4d9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (295) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [e1/5a87e2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [99/7f220c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [100%] 3 of 3 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (296) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [24/d0d6f0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 44%] 4 of 9 [df/f53128] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R2) [ 75%] 3 of 4 [fd/9d87d8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 44%] 4 of 9 [5c/9a0156] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R1) [ 75%] 3 of 4 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (297) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [24/d0d6f0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 44%] 4 of 9 [2f/61f1ea] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R1) [ 75%] 3 of 4 [fd/9d87d8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 44%] 4 of 9 [5c/9a0156] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R1) [ 75%] 3 of 4 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [3c/b959b4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R3) [ 89%] 17 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (297) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [24/d0d6f0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 44%] 4 of 9 [2f/61f1ea] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R1) [ 75%] 3 of 4 [fd/9d87d8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28-34C-R1) [ 44%] 4 of 9 [5c/9a0156] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R1) [ 75%] 3 of 4 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [2e/2f50c6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R1) [ 95%] 18 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (299) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [5d/26e8ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R1) [ 56%] 5 of 9 [78/20f115] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R1) [ 60%] 3 of 5 [7b/e0ead1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R1) [ 56%] 5 of 9 [fb/fc3a2d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R1) [ 60%] 3 of 5 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [2e/2f50c6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R1) [ 95%] 18 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (300) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [5d/26e8ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R1) [ 56%] 5 of 9 [78/20f115] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R1) [ 60%] 3 of 5 [c3/106c9d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R3) [ 67%] 6 of 9 [d3/ee5cc0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R3) [ 50%] 3 of 6 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [2e/2f50c6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R1) [ 95%] 18 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [5c/0e6f0e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (303) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [2e/2f50c6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R1) [ 95%] 18 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [32/af4d84] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (303) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [1f/235719] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [2e/2f50c6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R1) [ 95%] 18 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [32/af4d84] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (303) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e0/3ccec3] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [2e/2f50c6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R1) [ 95%] 18 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [32/af4d84] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (303) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e0/3ccec3] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 47%] 9 of 19 [a7/574129] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [f6/9305f2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R2) [ 78%] 7 of 9 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [32/af4d84] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (305) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [a8/9b4ac3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R1) [ 95%] 18 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e0/3ccec3] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [a3/839669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [32/af4d84] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [ac/a1f700] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R1) [ 68%] 13 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (305) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e0/3ccec3] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [a3/839669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [32/af4d84] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (305) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e0/3ccec3] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [a3/839669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d1/fb548f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (305) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e0/3ccec3] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [a3/839669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 89%] 17 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 84%] 16 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (305) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e0/3ccec3] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [a3/839669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [39/4d2c2e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28C-R2) [ 84%] 16 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (305) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e0/3ccec3] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [a3/839669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [ed/cb1ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R3) [ 58%] 11 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (305) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e0/3ccec3] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [a3/839669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [7f/4aa40e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (305) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 84%] 16 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [a3/839669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 70%] 7 of 10 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 43%] 3 of 7 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (305) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 84%] 16 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [f8/626c21] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 80%] 8 of 10 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [71/6dc409] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 80%] 8 of 10 [b5/25eaba] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (306) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 84%] 16 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [f8/626c21] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 80%] 8 of 10 [74/d75579] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R2) [ 38%] 3 of 8 [71/6dc409] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 80%] 8 of 10 [01/f559ab] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (307) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 84%] 16 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/16155f] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R3) [ 53%] 10 of 19 [f8/626c21] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 80%] 8 of 10 [3f/89b8d0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [71/6dc409] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R2) [ 80%] 8 of 10 [01/f559ab] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R2) [ 38%] 3 of 8 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (311) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 84%] 16 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [e1/5a87e2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [e9/8c81ea] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [67/6dc3bb] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [59/9b3b96] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (311) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [38/be203c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28C-R2) [ 84%] 16 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [e1/5a87e2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [e9/8c81ea] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [67/6dc3bb] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (311) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [e1/5a87e2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [e9/8c81ea] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [67/6dc3bb] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (311) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/3ecfdd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (are-120min-28C-R2) [ 88%] 21 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 90%] 19 of 21, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [e1/5a87e2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [e9/8c81ea] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [67/6dc3bb] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (311) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ae/f28572] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [e1/5a87e2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [e9/8c81ea] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 33%] 3 of 9 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [5c/9a0156] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R1) [ 44%] 4 of 9 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (313) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [e1/5a87e2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [2f/61f1ea] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R1) [ 44%] 4 of 9 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [5c/9a0156] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28-34C-R1) [ 44%] 4 of 9 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (313) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [e1/5a87e2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [78/20f115] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R1) [ 56%] 5 of 9 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [fb/fc3a2d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R1) [ 56%] 5 of 9 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (313) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [e1/5a87e2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [78/20f115] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R1) [ 56%] 5 of 9 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [d3/ee5cc0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R3) [ 67%] 6 of 9 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (314) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 91%] 10 of 11 [78/20f115] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R1) [ 50%] 5 of 10 [44/a7e03f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [d3/ee5cc0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R3) [ 67%] 6 of 9 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (315) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 91%] 10 of 11 [d1/0df716] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R3) [ 50%] 5 of 10 [a3/839669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 91%] 10 of 11 [24/cc617d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R3) [ 60%] 6 of 10 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (315) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [5c/5187b2] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 91%] 10 of 11 [6e/d9632c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R3) [ 60%] 6 of 10 [a3/839669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R3) [ 91%] 10 of 11 [24/cc617d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R3) [ 60%] 6 of 10 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (317) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [c1/4ce14e] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [42/1e865f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [ 64%] 7 of 11 [5d/3c582d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [d0/a54ef4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [ 64%] 7 of 11 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (317) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [c1/4ce14e] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [42/1e865f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [ 64%] 7 of 11 [5d/3c582d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [01/f559ab] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R2) [ 73%] 8 of 11 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (317) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [c1/4ce14e] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [e9/8c81ea] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [5d/3c582d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [67/6dc3bb] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (317) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [c1/4ce14e] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [e9/8c81ea] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [5d/3c582d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [67/6dc3bb] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [d1/50b91b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28C-R2) [ 84%] 16 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (317) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [c1/4ce14e] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [d1/0df716] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R3) [ 91%] 10 of 11 [5d/3c582d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [67/6dc3bb] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R1) [ 82%] 9 of 11 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/498fec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R3) [ 89%] 17 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (317) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [c1/4ce14e] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [d1/0df716] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R3) [ 91%] 10 of 11 [5d/3c582d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [d0/a54ef4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [100%] 11 of 11 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/498fec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R3) [ 89%] 17 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [33/2a44b6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (317) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [c1/4ce14e] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [42/1e865f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [100%] 11 of 11 [5d/3c582d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [d0/a54ef4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [100%] 11 of 11 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/498fec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R3) [ 89%] 17 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [82/335f31] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28C-R2) [ 84%] 16 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (317) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [56/8d2ab0] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R3) [ 58%] 11 of 19 [c1/4ce14e] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [42/1e865f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [100%] 11 of 11 [5d/3c582d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R3) [100%] 11 of 11 [d0/a54ef4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [100%] 11 of 11 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/498fec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R3) [ 89%] 17 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [00/e9ec0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R3) [ 89%] 17 of 19 [81/a8ed11] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (319) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d7/f48f98] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [c4/6e4f66] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [ 92%] 11 of 12 [42/1e865f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [100%] 11 of 11 [33/cc860d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [ 92%] 11 of 12 [d0/a54ef4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [100%] 11 of 11 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/498fec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R3) [ 89%] 17 of 19 [6f/d3dde5] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R1) [ 95%] 18 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [00/e9ec0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R3) [ 89%] 17 of 19 [07/c65b63] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28C-R2) [ 84%] 16 of 19 [cc/5cc567] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (319) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d7/f48f98] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [c4/6e4f66] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [ 92%] 11 of 12 [42/1e865f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [100%] 11 of 11 [33/cc860d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [ 92%] 11 of 12 [d0/a54ef4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R3) [100%] 11 of 11 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [00/e9ec0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R3) [ 89%] 17 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (321) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 91%] 20 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d7/f48f98] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [c4/6e4f66] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [100%] 12 of 12 [d9/c2f63f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [ 92%] 11 of 12 [33/cc860d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [100%] 12 of 12 [dc/72587f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [ 92%] 11 of 12 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [00/e9ec0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R3) [ 89%] 17 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (321) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d7/f48f98] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [c4/6e4f66] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [100%] 12 of 12 [d9/c2f63f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [ 92%] 11 of 12 [33/cc860d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [100%] 12 of 12 [dc/72587f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [ 92%] 11 of 12 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d9/f699e1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R3) [ 89%] 17 of 19 [00/e9ec0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R3) [ 89%] 17 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (321) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d7/f48f98] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [c4/6e4f66] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [100%] 12 of 12 [d9/c2f63f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [ 92%] 11 of 12 [33/cc860d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [100%] 12 of 12 [dc/72587f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [00/e9ec0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R3) [ 89%] 17 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (321) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [d7/f48f98] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [c4/6e4f66] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [100%] 12 of 12 [d9/c2f63f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [33/cc860d] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R1) [100%] 12 of 12 [dc/72587f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [00/e9ec0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R3) [ 89%] 17 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (323) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [ 92%] 12 of 13 [d9/c2f63f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [ 92%] 12 of 13 [dc/72587f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [00/e9ec0d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R3) [ 89%] 17 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [b1/4663d7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R1) [ 68%] 13 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (323) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [91/01402c] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [ 92%] 12 of 13 [d9/c2f63f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [ 92%] 12 of 13 [dc/72587f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (323) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [ 92%] 12 of 13 [d9/c2f63f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [ 92%] 12 of 13 [dc/72587f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (323) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [ 92%] 12 of 13 [d9/c2f63f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [ 92%] 12 of 13 [dc/72587f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [100%] 12 of 12 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (324) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [d9/c2f63f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R1) [ 92%] 12 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [ 92%] 12 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (325) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [ 92%] 12 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [ 92%] 12 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [29/3dd4e6] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28-34C-R1) [ 21%] 4 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (325) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [ 92%] 12 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [ 92%] 12 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 26%] 5 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (325) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [6d/eac3bb] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [83/100d85] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (are-120min-28C-R2) [ 95%] 21 of 22, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [ 92%] 12 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [ 92%] 12 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 26%] 5 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (327) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [ 92%] 12 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 26%] 5 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (327) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 26%] 5 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (327) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [8b/09ee24] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R1) [ 26%] 5 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (327) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 17 [10/03e15b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R1) [100%] 19 of 19, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [a9/8eb83d] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 6 [e2/35fe7c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [c5/2cdf6b] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R2) [ 32%] 6 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (330) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23, cached: 17 [d4/6af8f2] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [ac/f14e01] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 6 [cd/366f82] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [dc/7841ae] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R3) [ 37%] 7 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (330) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23, cached: 17 [d4/6af8f2] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [ac/f14e01] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 6 [cd/366f82] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [dc/7841ae] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R3) [ 37%] 7 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (330) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23, cached: 17 [d4/6af8f2] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [ac/f14e01] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 6 [cd/366f82] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [40/3a67bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [cc/084b90] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R3) [ 89%] 17 of 19 [64/1b6355] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (330) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [90/da0e0b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23, cached: 17 [d4/6af8f2] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [ac/f14e01] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 6 [cd/366f82] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [db/20dcf8] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R1) [ 68%] 13 of 19 [6a/4a3d94] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [d9/f0a484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R1) [100%] 13 of 13 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [40/3a67bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (335) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 91%] 21 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 90%] 19 of 21, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 90%] 19 of 21, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [ 93%] 13 of 14 [a2/b40f2a] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [ 93%] 13 of 14 [00/3fafaa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R1) [100%] 13 of 13 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [40/3a67bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [36/10b3e0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R1) [ 95%] 18 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (337) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 91%] 21 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 90%] 19 of 21, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 90%] 19 of 21, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [ 93%] 13 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [ 93%] 13 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [30/629d76] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R3) [ 47%] 9 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d4/006d59] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R1) [ 95%] 18 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (337) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 91%] 21 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 90%] 19 of 21, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 90%] 19 of 21, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [ 93%] 13 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [ 93%] 13 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (337) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 91%] 21 of 23, cached: 17 [d4/6af8f2] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 90%] 19 of 21, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 90%] 19 of 21, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [ 93%] 13 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [ 93%] 13 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [63/280828] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (337) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 91%] 21 of 23, cached: 17 [d4/6af8f2] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 90%] 19 of 21, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 90%] 19 of 21, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [ 93%] 13 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (337) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 91%] 21 of 23, cached: 17 [d4/6af8f2] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 90%] 19 of 21, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 90%] 19 of 21, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [47/c83f08] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/99c2ec] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R1) [ 95%] 18 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (337) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 91%] 21 of 23, cached: 17 [d4/6af8f2] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [65/b80f51] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 90%] 19 of 21, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 90%] 19 of 21, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (337) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [d3/a066d5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (are-120min-28C-R2) [ 91%] 21 of 23, cached: 17 [d4/6af8f2] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 90%] 19 of 21, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 90%] 19 of 21, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (340) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [0f/938609] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (340) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 84%] 16 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (340) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [29/cda7f8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28C-R2) [ 84%] 16 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (340) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [59/18d2ab] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [fe/90b4c4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (341) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [15/803376] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R3) [ 93%] 14 of 15 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [ee/81d8a1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [ 93%] 14 of 15 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (342) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [96/beb882] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [ 93%] 14 of 15 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [ee/81d8a1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [ 93%] 14 of 15 [06/017484] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [100%] 14 of 14 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (343) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [96/beb882] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [08/5294a4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R3) [ 93%] 14 of 15 [ee/81d8a1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [86/05441b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [ 93%] 14 of 15 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (344) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [96/beb882] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [b0/aff812] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [ 93%] 14 of 15 [ee/81d8a1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [86/05441b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [ 93%] 14 of 15 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (344) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [96/beb882] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [b0/aff812] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [ 93%] 14 of 15 [ee/81d8a1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [86/05441b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [ 93%] 14 of 15 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (344) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [96/beb882] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [b0/aff812] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [ 93%] 14 of 15 [ee/81d8a1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [86/05441b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (344) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [e3/f28cba] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [96/beb882] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [b0/aff812] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [ee/81d8a1] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [86/05441b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [d6/f07ac9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R1) [ 95%] 18 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (346) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 84%] 16 of 19 [f8/1a981f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R3) [ 94%] 15 of 16 [b0/aff812] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [d0/2ef434] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R3) [ 94%] 15 of 16 [86/05441b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R3) [100%] 15 of 15 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [93/c9a30f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R2) [ 58%] 11 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (348) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [de/e8f28b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 84%] 16 of 19 [f8/1a981f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R3) [100%] 16 of 16 [b7/e3acf6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [ 94%] 15 of 16 [d0/2ef434] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R3) [100%] 16 of 16 [f3/566a77] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [ 94%] 15 of 16 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (348) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 84%] 16 of 19 [f8/1a981f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R3) [100%] 16 of 16 [b7/e3acf6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [ 94%] 15 of 16 [d0/2ef434] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R3) [100%] 16 of 16 [f3/566a77] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [ 94%] 15 of 16 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (348) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 84%] 16 of 19 [f8/1a981f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R3) [100%] 16 of 16 [b7/e3acf6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [ 94%] 15 of 16 [d0/2ef434] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R3) [100%] 16 of 16 [f3/566a77] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [100%] 16 of 16 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (348) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [6b/ebf7e1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R3) [ 84%] 16 of 19 [f8/1a981f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R3) [100%] 16 of 16 [b7/e3acf6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [100%] 16 of 16 [d0/2ef434] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R3) [100%] 16 of 16 [f3/566a77] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [100%] 16 of 16 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (349) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [f8/1a981f] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R3) [ 94%] 16 of 17 [b7/e3acf6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [100%] 16 of 16 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [ 94%] 16 of 17 [f3/566a77] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [100%] 16 of 16 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (350) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [11/cec9ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R2) [ 94%] 16 of 17 [b7/e3acf6] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [100%] 16 of 16 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [ 94%] 16 of 17 [f3/566a77] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R3) [100%] 16 of 16 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (352) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [11/cec9ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [ 94%] 16 of 17 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [23/27b358] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [ 94%] 16 of 17 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (352) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [11/cec9ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [ 94%] 16 of 17 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [23/27b358] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [ 94%] 16 of 17 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (352) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [11/cec9ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [ 94%] 16 of 17 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [23/27b358] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (352) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [11/cec9ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [23/27b358] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [7d/9fb2e1] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (352) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [53/a5178f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 86%] 19 of 22, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [11/cec9ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [23/27b358] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (353) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [16/1f06c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [11/cec9ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [23/27b358] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (355) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [11/cec9ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [23/27b358] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (355) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [11/cec9ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [23/27b358] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [34/e366b0] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R3) [ 89%] 17 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (355) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [f7/8c3fc1] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28C-R2) [ 89%] 17 of 19 [11/cec9ef] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [da/9018ae] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28C-R2) [100%] 17 of 17 [23/27b358] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [19/643e12] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (357) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [b4/01ef50] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R1) [ 95%] 18 of 19 [6d/93ba43] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R1) [ 94%] 17 of 18 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [38/cbe7f3] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R1) [ 94%] 17 of 18 [23/27b358] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [100%] 17 of 17 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [19/643e12] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (358) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [b4/01ef50] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R1) [ 95%] 18 of 19 [6d/93ba43] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [6c/6f0a2b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28C-R2) [ 94%] 17 of 18 [38/cbe7f3] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [da/f88b48] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [ 94%] 17 of 18 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [19/643e12] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (359) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [b4/01ef50] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R1) [ 95%] 18 of 19 [6d/93ba43] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [50/a8bd27] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [ 94%] 17 of 18 [38/cbe7f3] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [da/f88b48] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [ 94%] 17 of 18 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [19/643e12] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (359) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [b4/01ef50] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R1) [ 95%] 18 of 19 [6d/93ba43] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [50/a8bd27] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [ 94%] 17 of 18 [38/cbe7f3] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [da/f88b48] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [ 94%] 17 of 18 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [19/643e12] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R1) [ 95%] 18 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (359) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [b4/01ef50] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R1) [ 95%] 18 of 19 [6d/93ba43] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [50/a8bd27] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [ 94%] 17 of 18 [38/cbe7f3] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [da/f88b48] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (359) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [b4/01ef50] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R1) [ 95%] 18 of 19 [6d/93ba43] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [50/a8bd27] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [38/cbe7f3] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [da/f88b48] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (359) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [b4/01ef50] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R1) [ 95%] 18 of 19 [6d/93ba43] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [50/a8bd27] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [38/cbe7f3] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [da/f88b48] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [bf/744074] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R1) [ 68%] 13 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (359) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [b4/01ef50] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R1) [ 95%] 18 of 19 [6d/93ba43] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [50/a8bd27] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [38/cbe7f3] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [da/f88b48] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [2a/6782bc] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R3) [ 74%] 14 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (359) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [b4/01ef50] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R1) [ 95%] 18 of 19 [6d/93ba43] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [50/a8bd27] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [38/cbe7f3] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R1) [100%] 18 of 18 [da/f88b48] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (361) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19 [50/a8bd27] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19 [da/f88b48] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R1) [100%] 18 of 18 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (363) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (363) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (363) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [ 95%] 18 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (363) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [2c/00774f] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R3) [ 79%] 15 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (363) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [cf/b42a11] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R3) [ 84%] 16 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (363) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [69/e660db] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R1) [ 89%] 17 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (363) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [20/c10f1f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 19 [4f/d13644] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [0d/413a4d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 95%] 18 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (365) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 95%] 18 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (365) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 95%] 18 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (365) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [ac/f14e01] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 16%] 3 of 19 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 95%] 18 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (365) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [ac/f14e01] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 21%] 4 of 19 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 95%] 18 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (365) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 21%] 4 of 19 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 95%] 18 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (365) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 21%] 4 of 19 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 95%] 18 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (366) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 21%] 4 of 19 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 95%] 18 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (367) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 21%] 4 of 19 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 95%] 18 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (367) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 21%] 4 of 19 [67/5b7f34] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28C-R2) [ 95%] 18 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (367) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a8/797be1] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28-34C-R1) [ 21%] 4 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (367) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 26%] 5 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (368) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED [ 0%] 0 of 1 [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 26%] 5 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (372) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [ 0%] 0 of 1 [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [ 0%] 0 of 1 [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [ 0%] 0 of 1 [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [ 0%] 0 of 1 [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 26%] 5 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (372) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [ 0%] 0 of 1 [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [ 0%] 0 of 1 [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [ 0%] 0 of 1 [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [ 0%] 0 of 1 [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 26%] 5 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (372) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [ 0%] 0 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [ 0%] 0 of 1 [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 26%] 5 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (372) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 26%] 5 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (372) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 17 [21/e5ef27] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 91%] 21 of 23, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 26%] 5 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (373) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [b4/574af2] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (are-120min-28C-R2) [ 88%] 21 of 24, cached: 6 [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 26%] 5 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (375) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [ 88%] 21 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 26%] 5 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (375) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [ 88%] 21 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [84/1c8808] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R2) [ 26%] 5 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (375) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [ 88%] 21 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6d/622c9e] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R2) [ 32%] 6 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (375) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 16 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [ 88%] 21 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 37%] 7 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (375) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS [ 0%] 0 of 2 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT [ 0%] 0 of 3 [- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS [ 0%] 0 of 3 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 37%] 7 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (386) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [81/269653] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R3) [ 0%] 0 of 24 [94/f9b97b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R1) [ 0%] 0 of 24 [b6/b83f90] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX3-120min-28C-R3) [ 0%] 0 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 37%] 7 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (396) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [90/b9aa70] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R2) [ 0%] 0 of 24 [be/83a31f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (VF36-120min-28-34C-R1) [ 0%] 0 of 24 [8e/d46903] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [ 0%] 0 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 37%] 7 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (407) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [94/5043b6] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 24 [1f/ec29ea] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (VF36-120min-28C-R1) [ 0%] 0 of 24 [62/39e184] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28C-R1) [ 0%] 0 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 37%] 7 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (417) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [b6/48e591] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28C-R3) [ 0%] 0 of 24 [e5/a26211] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (are-120min-28-34C-R3) [ 0%] 0 of 24 [86/2534e9] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28-34C-R2) [ 0%] 0 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 37%] 7 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (428) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [ab/301ad8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28C-R2) [ 0%] 0 of 24 [55/e726a7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28-34C-R1) [ 0%] 0 of 24 [26/afd0f8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX3-120min-28-34C-R1) [ 0%] 0 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 37%] 7 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (439) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [a7/d97d5b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28-34C-R1) [ 0%] 0 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [ 0%] 0 of 24 [b4/8c6f92] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R2) [ 0%] 0 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 37%] 7 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [73/409670] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [7f/73b45b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [66/ebc358] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R1) [ 37%] 7 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [73/409670] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [5f/4cdbf2] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX3-120min-28C-R1) [ 13%] 3 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [73/409670] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [5b/0a5a6f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28-34C-R1) [ 50%] 12 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [73/409670] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [86/2534e9] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28-34C-R2) [ 63%] 15 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [73/409670] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [4a/be5405] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX4-120min-28-34C-R1) [ 92%] 22 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [73/409670] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [7f/73b45b] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [73/409670] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [e5/a26211] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (are-120min-28-34C-R3) [ 4%] 1 of 24 [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [c8/eac17f] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R3) [ 8%] 2 of 24 [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [01/383e89] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R2) [ 33%] 8 of 24 [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [82/5c8f3d] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (are-120min-28-34C-R2) [ 50%] 12 of 24 [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f5/2803ae] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (are-120min-28C-R1) [ 71%] 17 of 24 [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [73/409670] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [96/90f189] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R3) [ 42%] 8 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [c2/d2432c] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (VF36-120min-28-34C-R2) [ 96%] 23 of 24 [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/cb8c53] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R3) [ 47%] 9 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/cb8c53] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R3) [ 47%] 9 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [92/c98cc5] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R3) [ 4%] 1 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [94/5043b6] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R3) [ 8%] 2 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [62/cb7171] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R2) [ 13%] 3 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [7b/71de8c] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [62/cb7171] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R2) [ 13%] 3 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7e/9634f6] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R1) [ 17%] 4 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [de/9a79c1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R1) [ 21%] 5 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [b6/48e591] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28C-R3) [ 29%] 7 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [50/514767] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28-34C-R2) [ 33%] 8 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [ef/ee739c] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28C-R1) [ 63%] 15 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [22/5d9b4d] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28C-R1) [ 71%] 17 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [ab/301ad8] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28C-R2) [ 75%] 18 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [b3/ad5818] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R1) [ 53%] 10 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [60/b9543e] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 58%] 11 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [54/1b7527] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28C-R2) [ 88%] 21 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 58%] 11 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [5d/44ea63] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 58%] 11 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [8d/1d6161] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28-34C-R2) [ 96%] 23 of 24 [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 58%] 11 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [ad/0dc452] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R3) [ 58%] 11 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [c8/116439] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R1) [ 63%] 12 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 68%] 13 of 19 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (447) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [cd/366f82] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 65%] 13 of 20 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [a2/17cc8a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (448) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 65%] 13 of 20 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [8f/877d9c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (449) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 62%] 13 of 21 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [6b/8541bd] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (450) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 62%] 13 of 21 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [af/0a5d1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [00/d3e284] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (452) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 62%] 13 of 21 [87/c7e629] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (453) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3f/cae965] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R1) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (454) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [cb/14e71a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (455) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (455) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (455) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (455) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [87/235679] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (456) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [18/f95755] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [71/5f040e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (458) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [14/d936dd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28-34C-R1) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [01/7c2f1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R2) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [76/041412] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (460) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [ad/b341c6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [76/041412] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (461) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [76/041412] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (462) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [4f/80f151] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [76/041412] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (464) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [76/041412] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (466) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [76/041412] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (467) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 62%] 13 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [76/041412] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (469) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [60/65d9a6] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R2) [ 62%] 13 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [60/65d9a6] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R2) [ 62%] 13 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [60/65d9a6] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R2) [ 62%] 13 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 67%] 14 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 67%] 14 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [ 95%] 20 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [df/ad6482] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R3) [ 67%] 14 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 90%] 19 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6f/744e35] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R3) [ 71%] 15 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [ad/b341c6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6f/744e35] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R3) [ 71%] 15 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [100%] 21 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [6f/744e35] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R3) [ 71%] 15 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 90%] 19 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [100%] 21 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [0f/b338f2] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R3) [ 76%] 16 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [e7/0893f7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [100%] 21 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [0f/b338f2] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R3) [ 76%] 16 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [100%] 21 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [100%] 21 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 81%] 17 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 90%] 19 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [100%] 21 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [100%] 21 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 81%] 17 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [100%] 21 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 90%] 19 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [100%] 21 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 81%] 17 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [100%] 21 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [01/7c2f1a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (are-120min-28C-R2) [ 95%] 20 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [100%] 21 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 81%] 17 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [a7/93841f] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [100%] 21 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [100%] 21 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [100%] 21 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [3e/eda7bf] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28C-R2) [ 81%] 17 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [100%] 21 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [100%] 21 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [100%] 21 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (471) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [c8/df4212] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (are-120min-28C-R2) [ 88%] 21 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [100%] 21 of 21, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 86%] 18 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [100%] 21 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [100%] 21 of 21 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [100%] 21 of 21 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [100%] 21 of 21 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 90%] 19 of 21 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (472) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [d7/2a3dcf] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (are-120min-28C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 90%] 19 of 21 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 86%] 18 of 21 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 90%] 19 of 21 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [100%] 21 of 21 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 95%] 21 of 22 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [ 95%] 21 of 22 [1c/c910b7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28C-R2) [ 95%] 21 of 22 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 90%] 19 of 21 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 90%] 19 of 21 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (474) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [00/7663a1] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 6 [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 82%] 18 of 22 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 86%] 19 of 22 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 95%] 21 of 22 [58/176673] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (are-120min-28C-R2) [ 95%] 21 of 22 [12/30cbe9] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (are-120min-28C-R2) [ 95%] 21 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 86%] 19 of 22 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (476) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 82%] 18 of 22 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 86%] 19 of 22 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 86%] 19 of 22 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (478) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 82%] 18 of 22 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 86%] 19 of 22 [47/75d56c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (are-120min-28C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (480) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [90/c67111] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R1) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (482) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [2b/49b0ba] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (are-120min-28C-R2) [ 91%] 20 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (483) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 91%] 20 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (483) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 91%] 20 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 91%] 20 of 22 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (483) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 91%] 20 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 91%] 20 of 22 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (483) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 95%] 21 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [f9/ec72f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28C-R2) [ 91%] 20 of 22 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (483) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 95%] 21 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [100%] 22 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 95%] 21 of 22 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (483) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 95%] 21 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 95%] 21 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [100%] 22 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 95%] 21 of 22 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 95%] 21 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (483) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 95%] 21 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [100%] 22 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 95%] 21 of 22 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 95%] 21 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (483) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 95%] 21 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [100%] 22 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [100%] 22 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 95%] 21 of 22 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 95%] 21 of 22 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (483) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [b5/442b32] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (VF36-120min-28-34C-R2) [ 92%] 22 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [100%] 22 of 22, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [01/02ea4d] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 82%] 18 of 22 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [100%] 22 of 22 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [100%] 22 of 22 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 95%] 21 of 22 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 91%] 21 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 86%] 19 of 22 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (484) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [aa/48e724] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (VF36-120min-28-34C-R2) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 78%] 18 of 23 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 91%] 21 of 23 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 91%] 21 of 23 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 91%] 21 of 23 [da/daa5c1] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (are-120min-28C-R2) [ 91%] 21 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (486) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 78%] 18 of 23 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 91%] 21 of 23 [97/d47298] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [0d/8084ff] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 91%] 21 of 23 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (489) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 78%] 18 of 23 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 91%] 21 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [4b/67db93] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (are-120min-28C-R2) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (490) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 78%] 18 of 23 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 91%] 21 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [57/3437cf] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (492) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 78%] 18 of 23 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 87%] 20 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (494) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [ 78%] 18 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 87%] 20 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (495) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [ 78%] 18 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 87%] 20 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (495) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [ 78%] 18 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 87%] 20 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (495) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [ 78%] 18 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 87%] 20 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (495) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [ 78%] 18 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (495) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [ 78%] 18 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (495) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [ 78%] 18 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (495) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [ 78%] 18 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (495) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [ 78%] 18 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (495) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (495) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [3b/0de898] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (496) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23 [cf/f95cb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [57/eaa0f4] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28-34C-R1) [ 95%] 19 of 20 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (497) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23 [cf/f95cb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [db/144523] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (497) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23 [cf/f95cb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20 [4f/e26669] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [db/144523] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20 [f5/ccf0b9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28-34C-R1) [100%] 19 of 19 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (499) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23 [cf/f95cb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [9d/0c449b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20 [db/144523] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [5d/f1cc13] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (499) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23 [cf/f95cb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [9d/0c449b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20 [db/144523] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [5d/f1cc13] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (499) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23 [cf/f95cb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [9d/0c449b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [db/144523] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [5d/f1cc13] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [ 95%] 19 of 20 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (499) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [01/c95866] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28C-R2) [ 87%] 20 of 23 [cf/f95cb0] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [9d/0c449b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [db/144523] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [5d/f1cc13] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 91%] 21 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (501) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [ 95%] 20 of 21 [9d/0c449b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [ 95%] 20 of 21 [5d/f1cc13] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (501) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [ 95%] 20 of 21 [9d/0c449b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [ 95%] 20 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [ 95%] 20 of 21 [5d/f1cc13] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28C-R2) [100%] 20 of 20 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (503) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [ 95%] 20 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [ 95%] 20 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (503) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [ 95%] 20 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [ 95%] 20 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (503) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [ 95%] 20 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (503) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6b/053676] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (503) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [f8/ea0746] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (503) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [fc/4924ac] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (are-120min-28C-R2) [ 91%] 21 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (503) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [e3/abd9f5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (503) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [51/f9df04] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (503) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [b7/581647] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (503) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/293f2e] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (are-120min-28C-R2) [ 91%] 21 of 23 [21/431288] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [31/ed00a5] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (are-120min-28C-R2) [100%] 21 of 21 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (505) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [1a/d7a902] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (506) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [66/53e470] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (are-120min-28C-R2) [100%] 21 of 21 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (507) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (507) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (507) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [ 95%] 21 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (507) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [cd/aefe80] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [3a/75b2e2] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (508) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 [e6/b989b3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [ca/344c90] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 83%] 19 of 23 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 83%] 19 of 23 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [c3/17e74e] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (511) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 79%] 19 of 24 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 79%] 19 of 24 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [44/909441] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (512) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 79%] 19 of 24 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 79%] 19 of 24 [ff/3e5e9a] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (514) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [20/8a1047] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (515) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [21/de3fc7] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [6f/ec9c3d] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (517) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [e8/5b2d5a] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28-34C-R1) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [89/114255] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (519) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (520) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (520) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (520) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (520) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [ 0%] 0 of 1 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (520) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (521) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [ 0%] 0 of 1 [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (521) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24, cached: 2 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (522) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS [ 0%] 0 of 9 [6e/283b58] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 9 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS [ 0%] 0 of 9 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (523) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [f8/5aa774] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 24 [6e/283b58] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R3) [ 0%] 0 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS [ 0%] 0 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (531) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [c5/7e79ec] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R1) [ 0%] 0 of 24 [87/2927a2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (are-120min-28-34C-R3) [ 0%] 0 of 24 [f9/411f39] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28-34C-R3) [ 0%] 0 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (540) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [9a/1240df] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R2) [ 0%] 0 of 24 [03/025ec9] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R2) [ 0%] 0 of 24 [89/fb9536] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX4-120min-28-34C-R2) [ 0%] 0 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (551) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [7f/64c954] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28-34C-R3) [ 0%] 0 of 24 [95/d4ce46] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28-34C-R2) [ 0%] 0 of 24 [44/bd30e6] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28C-R3) [ 0%] 0 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (560) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [08/eaf37c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28C-R1) [ 0%] 0 of 24 [7e/80637f] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (VF36-120min-28C-R1) [ 0%] 0 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [ 0%] 0 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (569) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [fd/4f2f63] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28C-R3) [ 0%] 0 of 24 [74/37af4d] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (VF36-120min-28C-R2) [ 0%] 0 of 24 [c0/5f029b] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX3-120min-28C-R3) [ 0%] 0 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (581) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [ac/c0ed45] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28C-R2) [ 0%] 0 of 24 [a7/a28879] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (are-120min-28C-R2) [ 0%] 0 of 24 [75/a20065] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX4-120min-28C-R2) [ 0%] 0 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (592) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f8/359c49] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [d3/054b2e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX4-120min-28-34C-R1) [ 0%] 0 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f8/359c49] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [dc/1d0d42] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f8/359c49] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f9/411f39] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28-34C-R3) [ 13%] 3 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f8/359c49] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [5f/35255c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX3-120min-28-34C-R3) [ 29%] 7 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f8/359c49] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [a0/613fc1] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R1) [ 50%] 12 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f8/359c49] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [07/fe92da] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R2) [ 63%] 15 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f8/359c49] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [dc/1d0d42] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (F3H-OX3-120min-28C-R2) [ 71%] 17 of 24 [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f8/359c49] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f8/359c49] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [87/2927a2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (are-120min-28-34C-R3) [ 4%] 1 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [6e/283b58] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R3) [ 8%] 2 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [03/f1cbc0] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (are-120min-28-34C-R1) [ 17%] 4 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [7e/80637f] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (VF36-120min-28C-R1) [ 54%] 13 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [7a/bd0de1] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (are-120min-28C-R1) [ 71%] 17 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [a7/a28879] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (are-120min-28C-R2) [ 83%] 20 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [07/bbdcc1] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28C-R2) [ 88%] 21 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [f8/359c49] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [10/57fac9] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28C-R2) [ 83%] 20 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 0%] 0 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [5b/35c649] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R3) [ 4%] 1 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [f8/5aa774] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R3) [ 8%] 2 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [d5/c884c3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R2) [ 13%] 3 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [d5/c884c3] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R2) [ 13%] 3 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [c5/7e79ec] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R1) [ 17%] 4 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [100%] 22 of 22 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (593) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [c5/7e79ec] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R1) [ 17%] 4 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [aa/2007ec] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [14/5cc88c] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (VF36-120min-28-34C-R2) [ 96%] 22 of 23 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (595) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [c5/7e79ec] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R1) [ 17%] 4 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [a4/44442b] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [8e/198bdc] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (VF36-120min-28-34C-R2) [100%] 22 of 22 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [c5/7e79ec] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28-34C-R1) [ 17%] 4 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [90/a5142e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28C-R3) [ 33%] 8 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [fd/4f2f63] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28C-R3) [ 50%] 12 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [ 96%] 22 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [fd/4f2f63] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28C-R3) [ 50%] 12 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [fd/4f2f63] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28C-R3) [ 50%] 12 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a3/d509da] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28-34C-R2) [ 54%] 13 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [01/a5b03c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28-34C-R3) [ 67%] 16 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [55/7e9d92] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28C-R1) [ 71%] 17 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [4f/8e382a] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28C-R2) [ 75%] 18 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [ba/fe03e9] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (are-120min-28C-R2) [ 83%] 20 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [97/ce4fcd] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX3-120min-28C-R2) [ 92%] 22 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [6b/3ee908] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28-34C-R2) [ 96%] 23 of 24 [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [6b/3ee908] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (VF36-120min-28-34C-R2) [ 96%] 23 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [bc/dc9220] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (are-120min-28C-R2) [ 88%] 21 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [0f/683d3c] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (597) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [96/2ab251] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [0b/5b7795] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (598) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [3d/c520c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (599) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [100%] 23 of 23 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (599) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [f1/4d66a9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [63/e00496] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [1f/ce5bc2] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 79%] 19 of 24 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [60/65d9a6] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R2) [ 83%] 20 of 24 [01/c96a18] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX4-120min-28-34C-R1) [ 96%] 23 of 24 [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [60/65d9a6] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (are-120min-28C-R2) [ 83%] 20 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: ... [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: ... [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: ... [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/05f153] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28C-R2) [ 88%] 21 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [86/504e19] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (VF36-120min-28-34C-R2) [ 92%] 22 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [bd/384dbd] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX3-120min-28C-R2) [ 96%] 23 of 24 [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC - executor > slurm (601) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC [ 0%] 0 of 1 executor > slurm (602) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [c3/7e3609] process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1) [ 0%] 0 of 1 executor > slurm (602) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [c3/7e3609] process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1) [ 0%] 0 of 1 executor > slurm (602) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [c3/7e3609] process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1) [100%] 1 of 1 ✔ -[nf-core/rnaseq] 24/24 samples passed STAR 5% mapped threshold: 89.64%: F3H-OX3-120min-28-34C-R1 89.9%: F3H-OX3-120min-28-34C-R2 88.98%: F3H-OX3-120min-28-34C-R3 89.47%: F3H-OX3-120min-28C-R1 90.04%: F3H-OX3-120min-28C-R3 89.89%: F3H-OX4-120min-28-34C-R2 ..see pipeline reports for full list - -[nf-core/rnaseq] Pipeline completed successfully- executor > slurm (602) [dc/c54e62] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [3f/fcb4c7] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS (rsem/S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [84/1aaf33] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [62/bd5ff4] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (S_lycopersicum_Sep_2019.fa) [100%] 1 of 1, cached: 1 ✔ [8c/af7b7f] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samples.csv) [100%] 1 of 1, cached: 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ - [35/6c1ecb] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [53/ea69db] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (are-120min-28C-R3) [100%] 24 of 24, cached: 24 ✔ [e8/400758] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 19 ✔ [db/4e5abd] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [d4/509ff1] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 16 ✔ [4d/0972a4] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [01/c0d4bc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [8e/3e4e20] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (are-120min-28C-R3) [100%] 24 of 24 ✔ [14/0ac68a] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 17 ✔ [7f/41de8f] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE (S_lycopersicum_Sep_2019.gtf) [100%] 1 of 1 ✔ [2a/22f43d] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT [100%] 1 of 1 ✔ [2e/5b82b8] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [33/6d6fb9] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [f3/a65675] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [58/5b76ab] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv) [100%] 1 of 1 ✔ [13/2705d2] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON [100%] 1 of 1 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [8e/568207] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 6 ✔ [9a/2011c2] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 3 ✔ [59/68acf5] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX (F3H-OX3-120min-28C-R2) [100%] 24 of 24, cached: 2 ✔ [a4/76d6be] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [4a/81794c] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [24/cca98e] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (VF36-120min-28-34C-R1) [100%] 24 of 24 ✔ [66/c56bd5] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [- ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [1f/91ed9a] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ea/6b35c9] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [a5/6b65fa] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [d9/215708] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [9a/ac97f8] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [43/3363a5] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (F3H-OX4-120min-28-34C-R1) [100%] 24 of 24 ✔ [e2/eabd98] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e6/00dcbc] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/68c512] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e7/846be4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [ab/f059c4] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [91/10d7f6] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [04/c53de8] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [5f/b1435b] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION (F3H-OX3-120min-28C-R2) [100%] 24 of 24 ✔ [e0/e4627b] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK [100%] 1 of 1 ✔ [13/b3fe70] process > NFCORE_RNASEQ:RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [c3/7e3609] process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1) [100%] 1 of 1 ✔ -[nf-core/rnaseq] 24/24 samples passed STAR 5% mapped threshold: 89.64%: F3H-OX3-120min-28-34C-R1 89.9%: F3H-OX3-120min-28-34C-R2 88.98%: F3H-OX3-120min-28-34C-R3 89.47%: F3H-OX3-120min-28C-R1 90.04%: F3H-OX3-120min-28C-R3 89.89%: F3H-OX4-120min-28-34C-R2 ..see pipeline reports for full list - -[nf-core/rnaseq] Pipeline completed successfully- Completed at: 28-Sep-2021 17:47:58 Duration : 1h 28m 57s CPU hours : 428.2 (50.8% cached) Succeeded : 602 Cached : 133