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  1. IGB
  2. IGBF-3043

Align and process rice RNA-Seq data using nf-core/rnaseq pipeline

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None
    • Story Points:
      2
    • Sprint:
      Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11

      Description

      Align and process RNA-Seq data using nf-core/rnaseq pipeline

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            ann.loraine Ann Loraine added a comment - - edited

            Pipeline halted very quickly after starting, choking on sample A.E.Y.S.2. Error appeared to be with pigz. Internet says this is a parallel implementation of gzip. Error message was:

            pigz: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
            

            Trying again:

            (nf-core) [aloraine@str-abm1 rna-seq]$ doIt.sh samplesheet_RNA-Seq.csv O_sativa_japonica_Oct_2011.fa O_sativa_japonica_Oct_2011.gtf O_sativa_japonica_Oct_2011.bed 2>5.err 1>5.out
            
            Show
            ann.loraine Ann Loraine added a comment - - edited Pipeline halted very quickly after starting, choking on sample A.E.Y.S.2. Error appeared to be with pigz. Internet says this is a parallel implementation of gzip. Error message was: pigz: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory Trying again: (nf-core) [aloraine@str-abm1 rna-seq]$ doIt.sh samplesheet_RNA-Seq.csv O_sativa_japonica_Oct_2011.fa O_sativa_japonica_Oct_2011.gtf O_sativa_japonica_Oct_2011.bed 2>5.err 1>5.out
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            New error on sample A.E.Y.S.3:

            Read 2 output is truncated at sequence count: 25069958, please check your paired-end input files! Terminating...
            

            Edited samples file to exclude R2 for A.E.Y.S.3 and tried again with:

            (nf-core) [aloraine@str-abm1 rna-seq]$ doIt.sh samplesheet_RNA-Seq.csv O_sativa_japonica_Oct_2011.fa O_sativa_japonica_Oct_2011.gtf O_sativa_japonica_Oct_2011.bed 2>6.err 1>6.out
            

            New error on A.E.Y.S.2:

            Read 2 output is truncated at sequence count: 28905992, please check your paired-end input files! Terminating...
            

            Edited samples file to exclude R2 for A.E.Y.S.2 and tried again with:

            (nf-core) [aloraine@str-abm1 rna-seq]$ doIt.sh samplesheet_RNA-Seq.csv O_sativa_japonica_Oct_2011.fa O_sativa_japonica_Oct_2011.gtf O_sativa_japonica_Oct_2011.bed 2>7.err 1>7.out 
            
            Show
            ann.loraine Ann Loraine added a comment - - edited New error on sample A.E.Y.S.3: Read 2 output is truncated at sequence count: 25069958, please check your paired-end input files! Terminating... Edited samples file to exclude R2 for A.E.Y.S.3 and tried again with: (nf-core) [aloraine@str-abm1 rna-seq]$ doIt.sh samplesheet_RNA-Seq.csv O_sativa_japonica_Oct_2011.fa O_sativa_japonica_Oct_2011.gtf O_sativa_japonica_Oct_2011.bed 2>6.err 1>6.out New error on A.E.Y.S.2: Read 2 output is truncated at sequence count: 28905992, please check your paired-end input files! Terminating... Edited samples file to exclude R2 for A.E.Y.S.2 and tried again with: (nf-core) [aloraine@str-abm1 rna-seq]$ doIt.sh samplesheet_RNA-Seq.csv O_sativa_japonica_Oct_2011.fa O_sativa_japonica_Oct_2011.gtf O_sativa_japonica_Oct_2011.bed 2>7.err 1>7.out
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            New error:

              yaml.scanner.ScannerError: mapping values are not allowed here
                in "versions.yml", line 23, column 21
            

            Tried again and got this result:

            -[nf-core/rnaseq] Pipeline completed successfully-
            Completed at: 03-Mar-2022 14:11:45
            Duration    : 1m 2s
            CPU hours   : 280.3 (100% cached)
            Succeeded   : 2
            Cached      : 534
            
            Show
            ann.loraine Ann Loraine added a comment - - edited New error: yaml.scanner.ScannerError: mapping values are not allowed here in "versions.yml" , line 23, column 21 Tried again and got this result: -[nf-core/rnaseq] Pipeline completed successfully- Completed at: 03-Mar-2022 14:11:45 Duration : 1m 2s CPU hours : 280.3 (100% cached) Succeeded : 2 Cached : 534
            Hide
            ann.loraine Ann Loraine added a comment -

            Checked bam output files in /nobackup/lorainelab/salty_rice/rna-seq/results/star_salmon.
            They are:

            A.C.N.R.1.sorted.bam  A.C.N.S.3.sorted.bam  A.E.N.R.2.sorted.bam  A.E.Y.S.2.sorted.bam  M.C.N.S.1.sorted.bam  M.E.N.R.3.sorted.bam
            A.C.N.R.2.sorted.bam  A.C.Y.S.1.sorted.bam  A.E.N.R.3.sorted.bam  A.E.Y.S.3.sorted.bam  M.C.N.S.2.sorted.bam  M.E.N.S.1.sorted.bam
            A.C.N.R.3.sorted.bam  A.C.Y.S.2.sorted.bam  A.E.N.S.1.sorted.bam  M.C.N.R.1.sorted.bam  M.C.N.S.3.sorted.bam  M.E.N.S.2.sorted.bam
            A.C.N.S.1.sorted.bam  A.C.Y.S.3.sorted.bam  A.E.N.S.2.sorted.bam  M.C.N.R.2.sorted.bam  M.E.N.R.1.sorted.bam  M.E.N.S.3.sorted.bam
            A.C.N.S.2.sorted.bam  A.E.N.R.1.sorted.bam  A.E.N.S.3.sorted.bam  M.C.N.R.3.sorted.bam  M.E.N.R.2.sorted.bam
            

            Multi-qc directory is also available.

            Requesting new first level review by Nowlan Freese.

            Show
            ann.loraine Ann Loraine added a comment - Checked bam output files in /nobackup/lorainelab/salty_rice/rna-seq/results/star_salmon. They are: A.C.N.R.1.sorted.bam A.C.N.S.3.sorted.bam A.E.N.R.2.sorted.bam A.E.Y.S.2.sorted.bam M.C.N.S.1.sorted.bam M.E.N.R.3.sorted.bam A.C.N.R.2.sorted.bam A.C.Y.S.1.sorted.bam A.E.N.R.3.sorted.bam A.E.Y.S.3.sorted.bam M.C.N.S.2.sorted.bam M.E.N.S.1.sorted.bam A.C.N.R.3.sorted.bam A.C.Y.S.2.sorted.bam A.E.N.S.1.sorted.bam M.C.N.R.1.sorted.bam M.C.N.S.3.sorted.bam M.E.N.S.2.sorted.bam A.C.N.S.1.sorted.bam A.C.Y.S.3.sorted.bam A.E.N.S.2.sorted.bam M.C.N.R.2.sorted.bam M.E.N.R.1.sorted.bam M.E.N.S.3.sorted.bam A.C.N.S.2.sorted.bam A.E.N.R.1.sorted.bam A.E.N.S.3.sorted.bam M.C.N.R.3.sorted.bam M.E.N.R.2.sorted.bam Multi-qc directory is also available. Requesting new first level review by Nowlan Freese .
            Hide
            nfreese Nowlan Freese added a comment - - edited

            All sorted bam files are present with file sizes that are in the range of what I would expect. I was able to download the multiqc_report.html and view it in a web browser.

            Show
            nfreese Nowlan Freese added a comment - - edited All sorted bam files are present with file sizes that are in the range of what I would expect. I was able to download the multiqc_report.html and view it in a web browser.

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              • Assignee:
                ann.loraine Ann Loraine
                Reporter:
                ann.loraine Ann Loraine
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                  Updated:
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