macs_annotatePeaks.mLb.clN.summary.txt file is not created

[FranBonath]

I am running the ATACseq pipeline on Rackham using singularity.
The genome is non-standard.

The pipeline crashes when the Macs peaks are supposed to be compared with the following error message:

[0;35m[nf-core/atacseq] Pipeline completed with errors
Error executing process > 'MergedLibPeakQC'
Caused by:
 Process `MergedLibPeakQC` terminated with an error exit status (1)
Command executed:
 plot_macs_qc.r \
   -i control_R1.mLb.clN_peaks.broadPeak,test_R2.mLb.clN_peaks.broadPeak,control_R2.mLb.clN_peaks.broadPeak,test_R1.mLb.clN_peaks.broadPeak,test_R3.mLb.clN_peaks.broadPeak,test_R4.mLb.clN_peaks.broadPeak,test_R5.mLb.clN_peaks.broadPeak,test_R6.mLb.clN_peaks.broadPeak \
   -s control_R1,test_R2,control_R2,test_R1,test_R3,test_R4,test_R5,test_R6 \
   -o ./ \
   -p macs_peak.mLb.clN
  
 plot_homer_annotatepeaks.r \
   -i control_R1.mLb.clN_peaks.annotatePeaks.txt,test_R2.mLb.clN_peaks.annotatePeaks.txt,test_R1.mLb.clN_peaks.annotatePeaks.txt,control_R2.mLb.clN_peaks.annotatePeaks.txt,test_R3.mLb.clN_peaks.annotatePeaks.txt,test_R4.mLb.clN_peaks.annotatePeaks.txt,test_R6.mLb.clN_peaks.annotatePeaks.txt,test_R5.mLb.clN_peaks.annotatePeaks.txt \
   -s control_R1,test_R2,test_R1,control_R2,test_R3,test_R4,test_R6,test_R5 \
   -o ./ \
   -p macs_annotatePeaks.mLb.clN
  
 cat mlib_peak_annotation_header.txt macs_annotatePeaks.mLb.clN.summary.txt > macs_annotatePeaks.mLb.clN.summary_mqc.tsv
Command exit status:
 1
Command output:
 null device 
      1 
Command error:
 cat: macs_annotatePeaks.mLb.clN.summary.txt: No such file or directory
Work dir:
 /crex/proj/sllstore2017079/private/fran/atacseq/ATAC_TSlotte/T.Slotte/work/23/db87d59f2347291ad31d1fea4a936e
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

The command used to run the pipeline on Rackham is as follows:
nextflow run nf-core/atacseq --input design_file.csv --gtf XXX_183_v1.0.gene.gtf --fasta XXX_183.fa --macs_gsize 150000 --save_reference --igenomes_ignore --project XXX -profile uppmax

attached are the *annotatePeaks.txt files, as requested.
troubleshooting_ATAC_annotatePeaks.tar.gz

[drpatelh]

@FranBonath This will be fixed in #74

Can you retry running the pipeline with -r dev when that PR has been merged please?

You may need to delete your local version of the pipeline first so the latest version is re-pulled at run-time:
rm -rf ~/.nextflow/assets/nf-core/atacseq/

[drpatelh]

Hi @FranBonath . Please feel free to reopen if you are still having issues running the dev version of the pipeline. Thanks!