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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
        • Epic Link:
        • 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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              Task - A task that needs to be done. IGBF-3099 Analyze differential expression using RNA-Seq

              • Major - Major loss of function.
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                28 older comments
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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
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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
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                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
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                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
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                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.

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                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 .
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                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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                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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