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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/4e02ab4e557de4cd6b33e3cccf64cd/.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/de/4e02ab4e557de4cd6b33e3cccf64cd/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz
==> STAGING COMPLETE (10 inputs)
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXYxbLVi/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXYxbLVi/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXYxbLVi/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:
/var/tmp/manta/runWorkflow.py
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXYxbLVi/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: /tmp/nxf.XXXXYxbLVi/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed.gz.tbi
[2026-06-08T20:33:17.296854Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Initiating pyFlow run
[2026-06-08T20:33:17.299547Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] pyFlowClientWorkflowClass: MantaWorkflow
[2026-06-08T20:33:17.299580Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] pyFlowVersion: 1.1.20
[2026-06-08T20:33:17.299586Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] pythonVersion: 2.7.15.final.0
[2026-06-08T20:33:17.299591Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] WorkingDir: '/tmp/nxf.XXXXYxbLVi'
[2026-06-08T20:33:17.299595Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] ProcessCmdLine: '/var/tmp/manta/runWorkflow.py -m local -j 14'
[2026-06-08T20:33:17.299603Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] [RunParameters] mode: local
[2026-06-08T20:33:17.299607Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] [RunParameters] nCores: 14
[2026-06-08T20:33:17.299611Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] [RunParameters] memMb: 3096076
[2026-06-08T20:33:17.299614Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] [RunParameters] dataDir: /var/tmp/manta/workspace/pyflow.data
[2026-06-08T20:33:17.299619Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] [RunParameters] isDryRun: False
[2026-06-08T20:33:17.299623Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] [RunParameters] isContinue: False
[2026-06-08T20:33:17.299626Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] [RunParameters] isForceContinue: True
[2026-06-08T20:33:17.299630Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] [RunParameters] mailTo: ''
[2026-06-08T20:33:17.300595Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:masterWorkflow] Starting task specification for master workflow
[2026-06-08T20:33:17.300648Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [MantaWorkflow] Initiating Manta workflow version: 1.6.0
[2026-06-08T20:33:17.300853Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'getAlignmentStats_makeTmpDir' to master workflow
[2026-06-08T20:33:17.301816Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'getAlignmentStats_generateStats_000' to master workflow
[2026-06-08T20:33:17.302382Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'getAlignmentStats_generateStats_001' to master workflow
[2026-06-08T20:33:17.302501Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'getAlignmentStats_mergeStats' to master workflow
[2026-06-08T20:33:17.302759Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'getAlignmentStats_removeTmpDir' to master workflow
[2026-06-08T20:33:17.302983Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'summarizeStats' to master workflow
[2026-06-08T20:33:17.303155Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'getAlignmentStats_makeTmpDir' from master workflow
[2026-06-08T20:33:17.303612Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'makeGraphTmpDir' to master workflow
[2026-06-08T20:33:17.308580Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:getAlignmentStats_makeTmpDir] Task initiated on local node
[2026-06-08T20:33:17.337434Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'getAlignmentStats_makeTmpDir' launched from master workflow
[2026-06-08T20:33:17.337884Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_001' from master workflow
[2026-06-08T20:33:17.338471Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'getAlignmentStats_generateStats_000' from master workflow
[2026-06-08T20:33:17.341948Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:getAlignmentStats_generateStats_001] Task initiated on local node
[2026-06-08T20:33:17.342936Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:getAlignmentStats_generateStats_000] Task initiated on local node
[2026-06-08T20:33:17.571804Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' to master workflow
[2026-06-08T20:33:17.818881Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' to master workflow
[2026-06-08T20:33:17.819137Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding sub-workflow task 'mergeLocusGraphInputList' to master workflow
[2026-06-08T20:33:17.819228Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'mergeLocusGraph' to master workflow
[2026-06-08T20:33:17.819304Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'checkLocusGraph' to master workflow
[2026-06-08T20:33:17.819371Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'removeTmpDir' to master workflow
[2026-06-08T20:33:17.819438Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'locusGraphStats' to master workflow
[2026-06-08T20:33:17.819662Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'makeHyGenDir' to master workflow
[2026-06-08T20:33:17.819782Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'generateCandidateSV_0000' to master workflow
[2026-06-08T20:33:17.819874Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortCandidateSV' to master workflow
[2026-06-08T20:33:17.819982Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding sub-workflow task 'sortCandidateSVInputList' to master workflow
[2026-06-08T20:33:17.820047Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'sort_sortCandidateSV' to master workflow
[2026-06-08T20:33:17.820111Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'tabix_sortCandidateSV' to master workflow
[2026-06-08T20:33:17.820176Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortDiploidSV' to master workflow
[2026-06-08T20:33:17.820271Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding sub-workflow task 'sortDiploidSVInputList' to master workflow
[2026-06-08T20:33:17.820341Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'sort_sortDiploidSV' to master workflow
[2026-06-08T20:33:17.820403Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'tabix_sortDiploidSV' to master workflow
[2026-06-08T20:33:17.820466Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'fixVcfHeader_sortSomaticSV' to master workflow
[2026-06-08T20:33:17.820561Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding sub-workflow task 'sortSomaticSVInputList' to master workflow
[2026-06-08T20:33:17.820625Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'sort_sortSomaticSV' to master workflow
[2026-06-08T20:33:17.820699Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'tabix_sortSomaticSV' to master workflow
[2026-06-08T20:33:17.820770Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'extractSmallIndels' to master workflow
[2026-06-08T20:33:17.820834Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'extractSmallIndels_tabix' to master workflow
[2026-06-08T20:33:17.820928Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding sub-workflow task 'sortEdgeRuntimeLogsInputList' to master workflow
[2026-06-08T20:33:17.820997Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Adding command task 'sortEdgeRuntimeLogs' to master workflow
[2026-06-08T20:33:17.821042Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
[2026-06-08T20:33:20.036798Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'getAlignmentStats_generateStats_000' launched from master workflow
[2026-06-08T20:33:23.558121Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'getAlignmentStats_generateStats_001' launched from master workflow
[2026-06-08T20:33:23.558693Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'getAlignmentStats_mergeStats' from master workflow
[2026-06-08T20:33:23.561822Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:getAlignmentStats_mergeStats] Task initiated on local node
[2026-06-08T20:33:23.622980Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'getAlignmentStats_mergeStats' launched from master workflow
[2026-06-08T20:33:23.623376Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'getAlignmentStats_removeTmpDir' from master workflow
[2026-06-08T20:33:23.623987Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'makeGraphTmpDir' from master workflow
[2026-06-08T20:33:23.624633Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'summarizeStats' from master workflow
[2026-06-08T20:33:23.628748Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:summarizeStats] Task initiated on local node
[2026-06-08T20:33:23.628942Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:getAlignmentStats_removeTmpDir] Task initiated on local node
[2026-06-08T20:33:23.630079Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:makeGraphTmpDir] Task initiated on local node
[2026-06-08T20:33:23.657742Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'getAlignmentStats_removeTmpDir' launched from master workflow
[2026-06-08T20:33:23.657801Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'makeGraphTmpDir' launched from master workflow
[2026-06-08T20:33:23.657825Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'summarizeStats' launched from master workflow
[2026-06-08T20:33:23.658148Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' from master workflow
[2026-06-08T20:33:23.658911Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' from master workflow
[2026-06-08T20:33:23.677108Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000] Task initiated on local node
[2026-06-08T20:33:23.678080Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000] Task initiated on local node
[2026-06-08T20:33:33.924404Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_020_chr21-5117103-5117231_0000_to_chromId_020_chr21-39269899-39270033_0000' launched from master workflow
[2026-06-08T20:33:40.793958Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'makeLocusGraph_chromId_020_chr21-39270283-39270433_0000_to_chromId_020_chr21-46664295-46664374_0000' launched from master workflow
[2026-06-08T20:33:40.795112Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching sub-workflow task: 'mergeLocusGraphInputList' from master workflow
[2026-06-08T20:33:40.795393Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:mergeLocusGraphInputList] Starting task specification for sub-workflow
[2026-06-08T20:33:40.795602Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:mergeLocusGraphInputList] Finished task specification for sub-workflow
[2026-06-08T20:33:40.796754Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed sub-workflow task: 'mergeLocusGraphInputList' launched from master workflow
[2026-06-08T20:33:40.797145Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'mergeLocusGraph' from master workflow
[2026-06-08T20:33:40.799974Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:mergeLocusGraph] Task initiated on local node
[2026-06-08T20:33:40.861394Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'mergeLocusGraph' launched from master workflow
[2026-06-08T20:33:40.861747Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'locusGraphStats' from master workflow
[2026-06-08T20:33:40.862376Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'checkLocusGraph' from master workflow
[2026-06-08T20:33:40.864954Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:locusGraphStats] Task initiated on local node
[2026-06-08T20:33:40.865184Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'removeTmpDir' from master workflow
[2026-06-08T20:33:40.865859Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:checkLocusGraph] Task initiated on local node
[2026-06-08T20:33:40.868191Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:removeTmpDir] Task initiated on local node
[2026-06-08T20:33:40.929555Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'locusGraphStats' launched from master workflow
[2026-06-08T20:33:40.929620Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'checkLocusGraph' launched from master workflow
[2026-06-08T20:33:40.929642Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'removeTmpDir' launched from master workflow
[2026-06-08T20:33:40.929960Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'makeHyGenDir' from master workflow
[2026-06-08T20:33:40.932688Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:makeHyGenDir] Task initiated on local node
[2026-06-08T20:33:40.994344Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'makeHyGenDir' launched from master workflow
[2026-06-08T20:33:40.994663Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'generateCandidateSV_0000' from master workflow
[2026-06-08T20:33:40.996786Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:generateCandidateSV_0000] Task initiated on local node
[2026-06-08T20:33:45.167333Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'generateCandidateSV_0000' launched from master workflow
[2026-06-08T20:33:45.167750Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching sub-workflow task: 'sortEdgeRuntimeLogsInputList' from master workflow
[2026-06-08T20:33:45.168004Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sortEdgeRuntimeLogsInputList] Starting task specification for sub-workflow
[2026-06-08T20:33:45.168184Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sortEdgeRuntimeLogsInputList] Finished task specification for sub-workflow
[2026-06-08T20:33:45.168773Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'fixVcfHeader_sortSomaticSV' from master workflow
[2026-06-08T20:33:45.169491Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'fixVcfHeader_sortCandidateSV' from master workflow
[2026-06-08T20:33:45.170088Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'fixVcfHeader_sortDiploidSV' from master workflow
[2026-06-08T20:33:45.173359Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:fixVcfHeader_sortCandidateSV] Task initiated on local node
[2026-06-08T20:33:45.173780Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed sub-workflow task: 'sortEdgeRuntimeLogsInputList' launched from master workflow
[2026-06-08T20:33:45.174031Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:fixVcfHeader_sortSomaticSV] Task initiated on local node
[2026-06-08T20:33:45.175514Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'sortEdgeRuntimeLogs' from master workflow
[2026-06-08T20:33:45.176129Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:fixVcfHeader_sortDiploidSV] Task initiated on local node
[2026-06-08T20:33:45.178267Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sortEdgeRuntimeLogs] Task initiated on local node
[2026-06-08T20:33:45.239810Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'fixVcfHeader_sortSomaticSV' launched from master workflow
[2026-06-08T20:33:45.239875Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'fixVcfHeader_sortDiploidSV' launched from master workflow
[2026-06-08T20:33:45.239897Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'sortEdgeRuntimeLogs' launched from master workflow
[2026-06-08T20:33:45.239918Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'fixVcfHeader_sortCandidateSV' launched from master workflow
[2026-06-08T20:33:45.240124Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching sub-workflow task: 'sortSomaticSVInputList' from master workflow
[2026-06-08T20:33:45.240463Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sortSomaticSVInputList] Starting task specification for sub-workflow
[2026-06-08T20:33:45.240713Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching sub-workflow task: 'sortDiploidSVInputList' from master workflow
[2026-06-08T20:33:45.240947Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sortSomaticSVInputList] Finished task specification for sub-workflow
[2026-06-08T20:33:45.241596Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sortDiploidSVInputList] Starting task specification for sub-workflow
[2026-06-08T20:33:45.241749Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sortDiploidSVInputList] Finished task specification for sub-workflow
[2026-06-08T20:33:45.241845Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching sub-workflow task: 'sortCandidateSVInputList' from master workflow
[2026-06-08T20:33:45.242543Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sortCandidateSVInputList] Starting task specification for sub-workflow
[2026-06-08T20:33:45.242769Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed sub-workflow task: 'sortSomaticSVInputList' launched from master workflow
[2026-06-08T20:33:45.242829Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed sub-workflow task: 'sortDiploidSVInputList' launched from master workflow
[2026-06-08T20:33:45.243162Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sortCandidateSVInputList] Finished task specification for sub-workflow
[2026-06-08T20:33:45.243457Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'sort_sortSomaticSV' from master workflow
[2026-06-08T20:33:45.243825Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'sort_sortDiploidSV' from master workflow
[2026-06-08T20:33:45.244166Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed sub-workflow task: 'sortCandidateSVInputList' launched from master workflow
[2026-06-08T20:33:45.244658Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'sort_sortCandidateSV' from master workflow
[2026-06-08T20:33:45.247044Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sort_sortDiploidSV] Task initiated on local node
[2026-06-08T20:33:45.248746Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sort_sortCandidateSV] Task initiated on local node
[2026-06-08T20:33:45.249321Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:sort_sortSomaticSV] Task initiated on local node
[2026-06-08T20:33:45.309025Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'sort_sortSomaticSV' launched from master workflow
[2026-06-08T20:33:45.309086Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'sort_sortDiploidSV' launched from master workflow
[2026-06-08T20:33:45.309108Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'sort_sortCandidateSV' launched from master workflow
[2026-06-08T20:33:45.309316Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'tabix_sortCandidateSV' from master workflow
[2026-06-08T20:33:45.309939Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'tabix_sortSomaticSV' from master workflow
[2026-06-08T20:33:45.310485Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'extractSmallIndels' from master workflow
[2026-06-08T20:33:45.312914Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'tabix_sortDiploidSV' from master workflow
[2026-06-08T20:33:45.313243Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:tabix_sortCandidateSV] Task initiated on local node
[2026-06-08T20:33:45.315510Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:tabix_sortSomaticSV] Task initiated on local node
[2026-06-08T20:33:45.316670Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:tabix_sortDiploidSV] Task initiated on local node
[2026-06-08T20:33:45.317909Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:extractSmallIndels] Task initiated on local node
[2026-06-08T20:33:45.346854Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'tabix_sortCandidateSV' launched from master workflow
[2026-06-08T20:33:45.346925Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'tabix_sortDiploidSV' launched from master workflow
[2026-06-08T20:33:45.346950Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'tabix_sortSomaticSV' launched from master workflow
[2026-06-08T20:33:45.362568Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'extractSmallIndels' launched from master workflow
[2026-06-08T20:33:45.362786Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Launching command task: 'extractSmallIndels_tabix' from master workflow
[2026-06-08T20:33:45.365505Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskRunner:extractSmallIndels_tabix] Task initiated on local node
[2026-06-08T20:33:45.394857Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [TaskManager] Completed command task: 'extractSmallIndels_tabix' launched from master workflow
[2026-06-08T20:33:50.920327Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Manta workflow successfully completed.
[2026-06-08T20:33:50.920327Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner]
[2026-06-08T20:33:50.920327Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] workflow version: 1.6.0
[2026-06-08T20:33:50.920426Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner]
[2026-06-08T20:33:50.920435Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Workflow successfully completed all tasks
[2026-06-08T20:33:50.920441Z] [nf-de4e02ab4e557de4cd6b33e3cccf64cd-dbb10-h5vsv] [612_1] [WorkflowRunner] Elapsed time for full workflow: 33 sec