macs_annotatePeaks.mLb.clN.summary.txt file is not created #73
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Description
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
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