Error executing process
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Description
Description of the bug
Hi
Can you please explain what would cause this error. Is it related to data quality?> i see on ataqv the tss score is low around 2.5 and this is for human hg19.
Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 137.
The full error message was:
Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_BAM_TO_BIGWIG:BEDTOOLS_GENOMECOV (2372962_A_1_REP1)'
Caused by:
Process NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_BAM_TO_BIGWIG:BEDTOOLS_GENOMECOV (2372962_A_1_REP1) terminated with an error exit status (137)
Command executed:
SCALE_FACTOR=$(grep '[0-9] mapped (' sample_1_REP1.mLb.clN.sorted.bam.flagstat | awk '{print 1000000/$1}')
echo $SCALE_FACTOR > sample_1_REP1.mLb.clN.scale_factor.txt
bedtools
genomecov
-ibam sample_1_REP1.mLb.clN.sorted.bam
-bg
-scale $SCALE_FACTOR
-pc
\
tmp.bg
bedtools sort -i tmp.bg > sample_1_REP1.mLb.clN.bedGraph
cat <<-END_VERSIONS > versions.yml
"NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_BAM_TO_BIGWIG:BEDTOOLS_GENOMECOV":
bedtools: $(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
Command exit status:
137
Command output:
(empty)
Command error:
.command.sh: line 14: 6719 Killed bedtools sort -i tmp.bg > sample_1_REP1.mLb.clN.bedGraph
Work dir:
/jobs/cscc-test-gkt6w-2/work/e8/b6cf43c3e547a94f0b069e3d7305c7
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
Command used and terminal output
Relevant files
No response
System information
No response
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start with the NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_BAM_TO_BIGWIG:BEDTOOLS_GENOMECOV process and inspect the failing .command.sh in the reported work directory. Check the bedtools genomecov and sort steps, the input BAM, and the complete command output to determine what caused exit status 137; done means identifying a reproducible cause and documenting the required fix or resource guidance.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- shell
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100