nf-core / nf-core/variantbenchmarking
Label change for process VCF_TO_CSV
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 51
- Forks
- 31
- Avg merge
- 1d 22h
- Merged PRs (30d)
- 1
Description
Description of the bug
Ran into this issue where pipeline was killed in the eighth of eight nf-NFCORE_VARIANTBENCHMARKING_VARIANTBENCHMARKING_COMPARE_BENCHMARK_RESULTS_VCF_TO_CSV jobs with exit status 137 indicating out of memory error. Pipeline completed successfully for me after labelling the VCF_TO_CSV process with process_low rather than process_single, felt it was worth raising the issue here for your consideration.
Command used and terminal output
Command used:
nextflow run /scratch/vbm/fork/variantbenchmarking -resume -profile docker -process.executor=slurm -process.queue=high \
--input ${SAMPLESHEET} \
--outdir ${OUTDIR} \
--analysis germline \
--variant_type snv \
--truth_id HG002 \
--truth_vcf /data/input/MGM/154/output/variantbenchmarking/resources/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz \
--regions_bed /data/input/MGM/154/output/variantbenchmarking/resources/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed \
--method happy,rtgtools \
--genome GRCh38 \
--fasta ${REF} \
--fai ${REF_FAI}
Terminal output:
ERROR ~ Error executing process > 'NFCORE_VARIANTBENCHMARKING:VARIANTBENCHMARKING:COMPARE_BENCHMARK_RESULTS:VCF_TO_CSV (rtgtools)'
Caused by:
Process `NFCORE_VARIANTBENCHMARKING:VARIANTBENCHMARKING:COMPARE_BENCHMARK_RESULTS:VCF_TO_CSV (rtgtools)` terminated with an error exit status (137)
Command executed:
vcf_to_csv.py \
rtgtools.TP_comp.vcf \
rtgtools.TP_comp.csv
Command exit status:
137
Command output:
(empty)
Command error:
.command.sh: line 4: 49 Killed vcf_to_csv.py rtgtools.TP_comp.vcf rtgtools.TP_comp.csv
Work dir:
/scratch/vbm/7481/work/51/4158dceb960f42f02c1a68d8007448
Container:
community.wave.seqera.io/library/pip_pandas:40d2e76c16c136f0
Relevant files
No response
System information
Nextflow version: 25.10.3
Hardware: HPC
Executor: slurm
Container engine: Docker
OS: Ubuntu
Version: 8b21c01749
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Locate the VCF_TO_CSV process definition in the variantbenchmarking pipeline and inspect how its process_single and process_low labels map to resources. Reproduce the reported workflow or examine the rtgtools job using the provided command, work directory, and exit-137 output. Done means the VCF_TO_CSV job completes without being killed for the reported workload.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, python
- Domain
- bioinformatics, infrastructure
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100