[2026-06-04T19:33:20.401073Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-04T19:33:20.401723Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-04T19:33:20.401747Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-04T19:33:20.401753Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-04T19:33:20.401759Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXlo3aU3'
[2026-06-04T19:33:20.401765Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-04T19:33:20.401771Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-04T19:33:20.401776Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-04T19:33:20.401781Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] [RunParameters] memMb: 1523736
[2026-06-04T19:33:20.401787Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-04T19:33:20.401794Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-04T19:33:20.401799Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-04T19:33:20.401804Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-04T19:33:20.401810Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-04T19:33:20.402327Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-04T19:33:20.402434Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-04T19:33:20.408252Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-04T19:33:20.408883Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-04T19:33:20.409120Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-04T19:33:20.409322Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-04T19:33:20.409551Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.411027Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.411201Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.411452Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.411841Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.412415Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.414363Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.414636Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-04T19:33:20.414979Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.415069Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.428457Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.428570Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.428645Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.428738Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.428811Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.428889Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.428975Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.429067Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.429142Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-04T19:33:20.429190Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-04T19:33:20.452150Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.452459Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.452805Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.453266Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.453902Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.457693Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:33:20.460103Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-04T19:33:20.461414Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-04T19:33:20.462003Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-04T19:33:20.568410Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.568494Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.568823Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.569136Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.571569Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:33:20.572335Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-04T19:33:20.601151Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.616812Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.617157Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T19:33:20.619626Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T19:33:20.681129Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:24.603804Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-04T19:33:24.604222Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-04T19:33:24.606637Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-04T19:33:24.636088Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.066782Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.067307Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.070141Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-04T19:36:55.131482Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.131732Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.131949Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.132285Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.132817Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.136433Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-04T19:36:55.138053Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-04T19:36:55.139010Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-04T19:36:55.197700Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.197806Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.197849Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.198174Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.198650Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.201479Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-04T19:36:55.202703Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-04T19:36:55.231759Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.235310Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.235632Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-04T19:36:55.238225Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-04T19:36:55.267504Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-04T19:37:08.688207Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-04T19:37:23.673679Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-04T19:37:23.673679Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] 
[2026-06-04T19:37:23.673679Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-06-04T19:37:23.673783Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] 
[2026-06-04T19:37:23.673792Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-04T19:37:23.673800Z] [nf-2f6efe2626a3b9bba78f9454fd325794-c3aaa-k5qb9] [713_1] [WorkflowRunner] Elapsed time for full workflow: 243 sec