Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/183aca9101d20af0d9d6cc2a172d0f/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/e3ed9d55ac1f3dfe6a268d860125cc/HCC1395_tumor_vs_HCC1395_BL.manta.candidate_small_indels.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_padded_intervals/scatter/chr21_34799195-34799564.bed.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/e3ed9d55ac1f3dfe6a268d860125cc/HCC1395_tumor_vs_HCC1395_BL.manta.candidate_small_indels.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/183aca9101d20af0d9d6cc2a172d0f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_padded_intervals/scatter/chr21_34799195-34799564.bed.gz
==> STAGING COMPLETE (12 inputs)


Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

/var/tmp/strelka/runWorkflow.py
[2026-06-08T20:44:37.243740Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-08T20:44:37.244769Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-08T20:44:37.244791Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-08T20:44:37.244799Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-08T20:44:37.244804Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXSnwhz4'
[2026-06-08T20:44:37.244809Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-08T20:44:37.244820Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-08T20:44:37.244824Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-08T20:44:37.244830Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] [RunParameters] memMb: 3096076
[2026-06-08T20:44:37.244835Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-08T20:44:37.244840Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-08T20:44:37.244846Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-08T20:44:37.244851Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-08T20:44:37.244856Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-08T20:44:37.245609Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-08T20:44:37.245718Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-08T20:44:37.251504Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-08T20:44:37.252320Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-08T20:44:37.252720Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-08T20:44:37.253129Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-08T20:44:37.253741Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.255111Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.255326Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.255400Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.255676Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.256212Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.256677Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.256906Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.257057Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.258984Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-08T20:44:37.270617Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.270743Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.270815Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.270902Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.270971Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.271044Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.271110Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.271186Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.271262Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-08T20:44:37.271306Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-08T20:44:37.292940Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.293245Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.293669Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.294285Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.295262Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.299672Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-08T20:44:37.301873Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-08T20:44:37.302917Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-08T20:44:37.304061Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-08T20:44:37.411352Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.411438Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.411805Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.412211Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.415641Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-08T20:44:37.417025Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-08T20:44:37.476335Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.476411Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.476748Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-08T20:44:37.480294Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-08T20:44:37.540992Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:38.607426Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-08T20:44:38.607789Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-08T20:44:38.610693Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-08T20:44:38.672137Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.545369Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.546127Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.549165Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-08T20:45:07.610734Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.610888Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.611009Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.611706Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.614139Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.614968Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-08T20:45:07.617954Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-08T20:45:07.618695Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-08T20:45:07.648494Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.648561Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.648583Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.648768Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.649035Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.652488Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-08T20:45:07.681590Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.681963Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-08T20:45:07.682966Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.683199Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-08T20:45:07.685806Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-08T20:45:07.715143Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-08T20:45:10.384283Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-08T20:45:25.364282Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-08T20:45:25.364282Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] 
[2026-06-08T20:45:25.364282Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-06-08T20:45:25.364386Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] 
[2026-06-08T20:45:25.364396Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-08T20:45:25.364404Z] [nf-94183aca9101d20af0d9d6cc2a172d0f-ad1c0-zpjlm] [675_1] [WorkflowRunner] Elapsed time for full workflow: 48 sec