nf-core / nf-core/variantbenchmarking

Label change for process VCF_TO_CSV

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enhancement
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

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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