nf-core / nf-core/atacseq

Error executing process

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bug
Dominant language
Nextflow
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13h 41m
Merged PRs (30d)
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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

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First steps

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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

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