Error executing process #421
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