File Info

Filename
.command.err
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/1cd2a7a894dc707302599ddebf6655/.command.err
Size
16.9 KB
Attempt
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXcosPYQ/chr21_34799195-34799564.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXcosPYQ/chr21_34799195-34799564.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXcosPYQ/chr21_34799195-34799564.bed.gz.tbi
[2026-06-04T17:19:28.567780Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-04T17:19:28.580026Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] pyFlowClientWorkflowClass: StrelkaSomaticWorkflow
[2026-06-04T17:19:28.580050Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-04T17:19:28.580056Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-04T17:19:28.580061Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXcosPYQ'
[2026-06-04T17:19:28.580065Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/strelka/runWorkflow.py -m local -j 8'
[2026-06-04T17:19:28.580070Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-04T17:19:28.580074Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] [RunParameters] nCores: 8
[2026-06-04T17:19:28.580077Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] [RunParameters] memMb: 1547931
[2026-06-04T17:19:28.580081Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/strelka/workspace/pyflow.data
[2026-06-04T17:19:28.580085Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-04T17:19:28.580088Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-04T17:19:28.580092Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-04T17:19:28.580096Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-04T17:19:28.580871Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-04T17:19:28.580930Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [StrelkaSomaticWorkflow] Initiating Strelka somatic workflow version: 2.9.10
[2026-06-04T17:19:28.586594Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding sub-workflow task 'CallGenome' to master workflow
[2026-06-04T17:19:28.587235Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching sub-workflow task: 'CallGenome' from master workflow
[2026-06-04T17:19:28.587540Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome] Starting task specification for sub-workflow
[2026-06-04T17:19:28.587795Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+makeTmpDir' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.588989Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-04T17:19:28.589101Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+makeTmpDir' from sub-workflow 'CallGenome'
[2026-06-04T17:19:28.590541Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.591994Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.592119Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.592350Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+makeTmpDir] Task initiated on local node
[2026-06-04T17:19:28.592555Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.592654Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.593068Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.593306Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.604953Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.605072Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.605147Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+completedAllGenomeSegments' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.605245Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.605323Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+SNV_index_vcf' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.605400Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_concat_vcf' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.605468Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+Indel_index_vcf' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.605552Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+mergeRunStats' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.605623Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Adding command task 'CallGenome+removeTmpDir' to sub-workflow 'CallGenome'
[2026-06-04T17:19:28.605668Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome] Finished task specification for sub-workflow
[2026-06-04T17:19:28.618436Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+makeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-04T17:19:28.618727Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T17:19:28.620416Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-04T17:19:28.620826Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T17:19:28.621319Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-04T17:19:28.621645Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-04T17:19:28.625656Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0003] Task initiated on local node
[2026-06-04T17:19:28.628371Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0002] Task initiated on local node
[2026-06-04T17:19:28.686594Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T17:19:28.686902Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T17:19:28.689603Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+fixVcfHeader_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T17:19:28.750977Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+fixVcfHeader_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T17:19:28.751235Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' from sub-workflow 'CallGenome'
[2026-06-04T17:19:28.753329Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0000] Task initiated on local node
[2026-06-04T17:19:28.783805Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0000' launched from sub-workflow 'CallGenome'
[2026-06-04T17:19:31.802798Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-04T17:19:31.803225Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' from sub-workflow 'CallGenome'
[2026-06-04T17:19:31.805874Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0002] Task initiated on local node
[2026-06-04T17:19:31.867249Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0002' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.659031Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+callGenomeSegment_chromId_020_chr21_0001] Task initiated on local node
[2026-06-04T17:22:01.698698Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.698769Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+callGenomeSegment_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.699425Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.699933Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.702659Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0003] Task initiated on local node
[2026-06-04T17:22:01.703737Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+compressSegmentOutput_chromId_020_chr21_0001] Task initiated on local node
[2026-06-04T17:22:01.765430Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0003' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.765482Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+compressSegmentOutput_chromId_020_chr21_0001' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.765597Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+completedAllGenomeSegments' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.765711Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+mergeRunStats' from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.766196Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+Indel_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.769176Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+Indel_concat_vcf] Task initiated on local node
[2026-06-04T17:22:01.769621Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+SNV_concat_vcf' from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.770241Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+mergeRunStats] Task initiated on local node
[2026-06-04T17:22:01.772221Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+SNV_concat_vcf] Task initiated on local node
[2026-06-04T17:22:01.801725Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+SNV_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.801790Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+Indel_concat_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.801814Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+mergeRunStats' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.801988Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+SNV_index_vcf' from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.803456Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+Indel_index_vcf' from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.804138Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+SNV_index_vcf] Task initiated on local node
[2026-06-04T17:22:01.806161Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+Indel_index_vcf] Task initiated on local node
[2026-06-04T17:22:01.835291Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+SNV_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.835341Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+Indel_index_vcf' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.835494Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Launching command task: 'CallGenome+removeTmpDir' from sub-workflow 'CallGenome'
[2026-06-04T17:22:01.837667Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskRunner:CallGenome+removeTmpDir] Task initiated on local node
[2026-06-04T17:22:01.867464Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed command task: 'CallGenome+removeTmpDir' launched from sub-workflow 'CallGenome'
[2026-06-04T17:22:16.791062Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [TaskManager] Completed sub-workflow task: 'CallGenome' launched from master workflow
[2026-06-04T17:22:16.800997Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Strelka somatic workflow successfully completed.
[2026-06-04T17:22:16.800997Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] 
[2026-06-04T17:22:16.800997Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] 	workflow version: 2.9.10
[2026-06-04T17:22:16.801044Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] 
[2026-06-04T17:22:16.801053Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-04T17:22:16.801061Z] [nf-1c1cd2a7a894dc707302599ddebf6655-236e3-dfxvg] [657_1] [WorkflowRunner] Elapsed time for full workflow: 168 sec