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Illumina / strelka

Strelka2 germline and somatic small variant caller
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Meaning of taskExitCode -9 #232

Open Jessime opened 1 year ago

Jessime commented 1 year ago

Hi, I'm trying strelka (version 2.9.10), and I'm running into an issue I'm having trouble debugging. The error is:

$ cat strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/041/pyflowTaskWrapper.signal.txt

[2023-07-31T23:51:21.730936Z] [1b03a2a20c84] [330_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_011_chr12_0001] [wrapperSignal] wrapperStart
[2023-07-31T23:51:21.749836Z] [1b03a2a20c84] [330_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_011_chr12_0001] [wrapperSignal] taskStart
[2023-07-31T23:51:24.954597Z] [1b03a2a20c84] [330_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_011_chr12_0001] [wrapperSignal] taskExitCode -9
[2023-07-31T23:51:24.959961Z] [1b03a2a20c84] [330_1] [pyflowTaskWrapper:CallGenome+callGenomeSegment_chromId_011_chr12_0001] [wrapperSignal] taskStderrTail 1
Last 0 stderr lines from task (of 0 total lines):

which doesn't give me much to go off of. The subtask command is:

/usr/local/share/strelka-2.9.10-1/libexec/starling2 \
    --region chr12:11106277-22212552 \
    --ref Homo_sapiens_assembly38.fasta \
    --max-indel-size 49 \
    --call-regions-bed chr11_126463157-126463307.bed.gz \
    --min-mapping-quality 20 \
    --gvcf-output-prefix strelka/workspace/genomeSegment.tmpdir/segment.chromId_011_chr12_0001. \
    --gvcf-min-gqx 15 \
    --gvcf-min-homref-gqx 15 \
    --gvcf-max-snv-strand-bias 10 \
    --enable-read-backed-phasing \
    --stats-file strelka/workspace/genomeSegment.tmpdir/runStats.chromId_011_chr12_0001.xml \
    --align-file 21_230142.recal.cram \
    --gvcf-skip-header \
    --indel-error-models-file /usr/local/share/strelka-2.9.10-1/share/config/indelErrorModel.json \
    --theta-file /usr/local/share/strelka-2.9.10-1/share/config/theta.json

Also, as far as I can tell, the task only fails if I'm running from pyflow. If I shell into the quay.io/biocontainers/strelka container, and run the above command directly, it runs without issue (although, it produces an empty vcf).

Any hints on how I could start debugging this would be helpful, thanks!

juanesarango commented 2 months ago

I'm getting the same error. Running with toil. I suspect taskExitCode -9 is a memory issue. But I haven't been able to overcome it yet, despite increasing it.