Strelka failed to complete command task #250
Description
Hi,
I'm using Strelka (Strelka somatic workflow version: 2.9.10) inside a pipeline, running on a hpc cluster. Resources are menaged by slurm. I cannot solve this error:
[TaskManager] [ERROR] Failed to complete command task: 'CallGenome+callGenomeSegment_chromId_003_chr4_0013' launched from sub-workflow 'CallGenome', error code: 1, command: '/home/fguana/.conda/envs/strelka2/share/strelka-2.9.10-2/libexec/strelka2 --region chr4:154549329-166437737 --ref /home/fguana/resources/reference_genome/noalt/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa --max-indel-size 49 --call-regions-bed /home/fguana/resources/bedfiles_wes_pdx/xgen-exome-hyb-panel-v2-targets-hg38.bed.gz --min-mapping-quality 20 --somatic-snv-rate 0.0001 --shared-site-error-rate 0.0000000005 --shared-site-error-strand-bias-fraction 0.0 --somatic-indel-rate 0.000001 --shared-indel-error-factor 2.2 --tier2-min-mapping-quality 0 --strelka-snv-max-filtered-basecall-frac 0.4 --strelka-snv-max-spanning-deletion-frac 0.75 --strelka-snv-min-qss-ref 15 --strelka-indel-max-window-filtered-basecall-frac 0.3 --strelka-indel-min-qsi-ref 40 --ssnv-contam-tolerance 0.15 --indel-contam-tolerance 0.15 --somatic-snv-scoring-model-file /home/fguana/.conda/envs/strelka2/share/strelka-2.9.10-2/share/config/somaticSNVScoringModels.json --somatic-indel-scoring-model-file /home/fguana/.conda/envs/strelka2/share/strelka-2.9.10-2/share/config/somaticIndelScoringModels.json --normal-align-file /home/fguana/tempfiles/PMP_01_044_met_tg/PMP_01_044_blood_tg.sorted.markdup.bqsrecal.bam --tumor-align-file /home/fguana/tempfiles/PMP_01_044_met_tg/PMP_01_044_met_tg.sorted.markdup.bqsrecal.bam --somatic-snv-file /home/fguana/tempfiles/PMP_01_044_met_tg/Strelka_calling/workspace/genomeSegment.tmpdir/somatic.snvs.unfiltered.chromId_003_chr4_0013.vcf --somatic-indel-file /home/fguana/tempfiles/PMP_01_044_met_tg/Strelka_calling/workspace/genomeSegment.tmpdir/somatic.indels.unfiltered.chromId_003_chr4_0013.vcf --stats-file /home/fguana/tempfiles/PMP_01_044_met_tg/Strelka_calling/workspace/genomeSegment.tmpdir/runStats.chromId_003_chr4_0013.xml --strelka-skip-header'
I add the complete log files
PMP_044_met.log
I tried to change slurm parameters about memory request but I had the same error.
Could you give me any suggestion to solve the problem?