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April 20, 2018 19:26
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Cromwell bcbio no docker debugging
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| Script started on Fri 20 Apr 2018 03:17:41 PM EDT | |
| $ bash run_cromwell.sh | |
| Running: export PATH=$PATH:/usr/local/share/bcbio-vm/bin && cromwell run --type CWL --inputs /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/main-somatic-samples.json /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/main-somatic.cwl 2>&1 | tee -a /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-cromwell.log | |
| [2018-04-20 15:17:47,33] [info] Running with database db.url = jdbc:hsqldb:mem:fea1cf43-9434-4085-b283-d40102cc76c8;shutdown=false;hsqldb.tx=mvcc | |
| [2018-04-20 15:17:52,71] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000 | |
| [2018-04-20 15:17:52,72] [info] [RenameWorkflowOptionsInMetadata] 100% | |
| [2018-04-20 15:17:52,83] [info] Running with database db.url = jdbc:hsqldb:mem:7405ca2a-863a-4e13-afad-b8e006f849e1;shutdown=false;hsqldb.tx=mvcc | |
| [2018-04-20 15:17:53,24] [info] Slf4jLogger started | |
| [2018-04-20 15:17:53,26] [info] Pre Processing Workflow... | |
| [2018-04-20 15:17:53,45] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/main-somatic.cwl | |
| [2018-04-20 15:17:55,14] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/alignment_to_rec.cwl | |
| [2018-04-20 15:17:56,54] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/wf-alignment.cwl | |
| [2018-04-20 15:17:57,79] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/prep_align_inputs.cwl | |
| [2018-04-20 15:17:59,19] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/process_alignment.cwl | |
| [2018-04-20 15:18:00,70] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/prep_samples_to_rec.cwl | |
| [2018-04-20 15:18:02,05] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/prep_samples.cwl | |
| [2018-04-20 15:18:03,40] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/postprocess_alignment_to_rec.cwl | |
| [2018-04-20 15:18:05,18] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/postprocess_alignment.cwl | |
| [2018-04-20 15:18:06,65] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/combine_sample_regions.cwl | |
| [2018-04-20 15:18:08,24] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/batch_for_variantcall.cwl | |
| [2018-04-20 15:18:09,67] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/wf-variantcall.cwl | |
| [2018-04-20 15:18:10,96] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/get_parallel_regions.cwl | |
| [2018-04-20 15:18:12,35] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/variantcall_batch_region.cwl | |
| [2018-04-20 15:18:13,94] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/concat_batch_variantcalls.cwl | |
| [2018-04-20 15:18:15,42] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/postprocess_variants.cwl | |
| [2018-04-20 15:18:16,78] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/compare_to_rm.cwl | |
| [2018-04-20 15:18:18,19] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/summarize_vc.cwl | |
| [2018-04-20 15:18:19,60] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/qc_to_rec.cwl | |
| [2018-04-20 15:18:21,00] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/pipeline_summary.cwl | |
| [2018-04-20 15:18:22,45] [info] Pre-Processing /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/somatic-workflow-nodocker/steps/multiqc_summary.cwl | |
| [2018-04-20 15:18:23,84] [info] Pre Processing Inputs... | |
| [2018-04-20 15:18:23,99] [info] Workflow heartbeat configuation: | |
| { | |
| "cromwellId" : "cromid-25fedf0", | |
| "heartbeatInterval" : "2 minutes", | |
| "ttl" : "10 minutes", | |
| "writeBatchSize" : 10000, | |
| "writeThreshold" : 10000 | |
| } | |
| [2018-04-20 15:18:24,05] [info] Metadata summary refreshing every 2 seconds. | |
| [2018-04-20 15:18:24,08] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. | |
| [2018-04-20 15:18:24,09] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. | |
| [2018-04-20 15:18:24,09] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. | |
| [2018-04-20 15:18:24,80] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. | |
| [2018-04-20 15:18:24,82] [info] SingleWorkflowRunnerActor: Submitting workflow | |
| [2018-04-20 15:18:24,87] [info] CWL (Unspecified version) workflow b349aa40-9376-47ab-a345-86745a8545b6 submitted | |
| [2018-04-20 15:18:24,87] [info] SingleWorkflowRunnerActor: Workflow submitted [38;5;2mb349aa40-9376-47ab-a345-86745a8545b6[0m | |
| [2018-04-20 15:18:24,88] [info] 1 new workflows fetched | |
| [2018-04-20 15:18:24,88] [info] WorkflowManagerActor Starting workflow [38;5;2mb349aa40-9376-47ab-a345-86745a8545b6[0m | |
| [2018-04-20 15:18:24,89] [info] WorkflowManagerActor Successfully started WorkflowActor-b349aa40-9376-47ab-a345-86745a8545b6 | |
| [2018-04-20 15:18:24,89] [info] Retrieved 1 workflows from the WorkflowStoreActor | |
| [2018-04-20 15:18:24,90] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. | |
| [2018-04-20 15:18:26,85] [info] MaterializeWorkflowDescriptorActor [[38;5;2mb349aa40[0m]: Call-to-Backend assignments: get_parallel_regions -> Local, prep_align_inputs -> Local, postprocess_alignment -> Local, pipeline_summary -> Local, prep_samples_to_rec -> Local, summarize_vc -> Local, compare_to_rm -> Local, postprocess_variants -> Local, postprocess_alignment_to_rec -> Local, concat_batch_variantcalls -> Local, combine_sample_regions -> Local, alignment_to_rec -> Local, multiqc_summary -> Local, process_alignment -> Local, qc_to_rec -> Local, batch_for_variantcall -> Local, prep_samples -> Local, variantcall_batch_region -> Local | |
| [2018-04-20 15:18:27,13] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,14] [[38;5;220mwarn[0m] Couldn't find a suitable DSN, defaulting to a Noop one. | |
| [2018-04-20 15:18:27,15] [info] Using noop to send events. | |
| [2018-04-20 15:18:27,19] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,20] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,20] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,20] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,20] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,20] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,21] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,21] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,21] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,21] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,21] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,21] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,21] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,21] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,21] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,22] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:27,22] [[38;5;220mwarn[0m] Local [[38;5;2mb349aa40[0m]: Key/s [memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-04-20 15:18:29,43] [info] WorkflowExecutionActor-b349aa40-9376-47ab-a345-86745a8545b6 [[38;5;2mb349aa40[0m]: Starting alignment_to_rec, prep_samples_to_rec | |
| [2018-04-20 15:18:29,89] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0malignment_to_rec:NA:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:29,90] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples_to_rec:NA:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:30,30] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0malignment_to_rec:NA:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'alignment_to_rec' 'cwl' 'sentinel_runtime=cores,1,ram,2048' 'sentinel_parallel=multi-combined' 'sentinel_outputs=alignment_rec:resources;description;config__algorithm__align_split_size;files;config__algorithm__trim_reads;reference__fasta__base;config__algorithm__adapters;rgnames__lb;rgnames__rg;rgnames__lane;config__algorithm__bam_clean;config__algorithm__aligner;reference__minimap2__indexes;rgnames__pl;rgnames__pu;config__algorithm__mark_duplicates;analysis;rgnames__sample' 'sentinel_inputs=files:var,analysis:var,config__algorithm__align_split_size:var,reference__fasta__base:var,rgnames__pl:var,rgnames__sample:var,rgnames__pu:var,rgnames__lane:var,rgnames__rg:var,rgnames__lb:var,reference__minimap2__indexes:var,config__algorithm__aligner:var,config__algorithm__trim_reads:var,config__algorithm__adapters:var,config__algorithm__bam_clean:var,config__algorithm__mark_duplicates:var,resources:var,description:var'[0m | |
| [2018-04-20 15:18:30,30] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples_to_rec:NA:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'prep_samples_to_rec' 'cwl' 'sentinel_runtime=cores,1,ram,2048' 'sentinel_parallel=multi-combined' 'sentinel_outputs=prep_samples_rec:resources;description;reference__fasta__base;config__algorithm__coverage;config__algorithm__variant_regions' 'sentinel_inputs=config__algorithm__coverage:var,config__algorithm__variant_regions:var,reference__fasta__base:var,resources:var,description:var'[0m | |
| [2018-04-20 15:18:30,37] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0malignment_to_rec:NA:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-alignment_to_rec/execution/script | |
| [2018-04-20 15:18:30,37] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples_to_rec:NA:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-prep_samples_to_rec/execution/script | |
| [2018-04-20 15:18:34,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0malignment_to_rec:NA:1]: job id: 15789 | |
| [2018-04-20 15:18:34,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples_to_rec:NA:1]: job id: 15786 | |
| [2018-04-20 15:18:34,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples_to_rec:NA:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:34,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0malignment_to_rec:NA:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:36,96] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples_to_rec:NA:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:18:38,34] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0malignment_to_rec:NA:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:18:39,69] [info] WorkflowExecutionActor-b349aa40-9376-47ab-a345-86745a8545b6 [[38;5;2mb349aa40[0m]: Starting prep_samples (3 shards) | |
| [2018-04-20 15:18:39,86] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:0:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:39,87] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:1:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:39,88] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:2:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:39,90] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:0:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'prep_samples' 'cwl' 'sentinel_runtime=cores,1,ram,2048' 'sentinel_parallel=multi-parallel' 'sentinel_outputs=config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready' 'sentinel_inputs=prep_samples_rec:record'[0m | |
| [2018-04-20 15:18:39,90] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:2:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'prep_samples' 'cwl' 'sentinel_runtime=cores,1,ram,2048' 'sentinel_parallel=multi-parallel' 'sentinel_outputs=config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready' 'sentinel_inputs=prep_samples_rec:record'[0m | |
| [2018-04-20 15:18:39,91] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:0:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-prep_samples/shard-0/execution/script | |
| [2018-04-20 15:18:39,91] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:1:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'prep_samples' 'cwl' 'sentinel_runtime=cores,1,ram,2048' 'sentinel_parallel=multi-parallel' 'sentinel_outputs=config__algorithm__variant_regions,config__algorithm__variant_regions_merged,config__algorithm__variant_regions_orig,config__algorithm__coverage,config__algorithm__coverage_merged,config__algorithm__coverage_orig,config__algorithm__seq2c_bed_ready' 'sentinel_inputs=prep_samples_rec:record'[0m | |
| [2018-04-20 15:18:39,91] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:2:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-prep_samples/shard-2/execution/script | |
| [2018-04-20 15:18:39,91] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:1:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-prep_samples/shard-1/execution/script | |
| [2018-04-20 15:18:42,79] [info] b07cdb7e-f4e7-4c47-ab9a-bd6756d18b92-SubWorkflowActor-SubWorkflow-alignment:1:1 [[38;5;2mb07cdb7e[0m]: Starting prep_align_inputs | |
| [2018-04-20 15:18:42,79] [info] 150711af-1057-4268-b49e-8c2fa3553ebd-SubWorkflowActor-SubWorkflow-alignment:0:1 [[38;5;2m150711af[0m]: Starting prep_align_inputs | |
| [2018-04-20 15:18:42,79] [info] 559b1695-f115-4008-b14e-a7ba4d488314-SubWorkflowActor-SubWorkflow-alignment:2:1 [[38;5;2m559b1695[0m]: Starting prep_align_inputs | |
| [2018-04-20 15:18:42,82] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprep_align_inputs:NA:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:42,82] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprep_align_inputs:NA:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:42,82] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprep_align_inputs:NA:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:42,84] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprep_align_inputs:NA:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'prep_align_inputs' 'cwl' 'sentinel_runtime=cores,2,ram,4096' 'sentinel_parallel=single-single' 'sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split' 'sentinel_inputs=alignment_rec:record'[0m | |
| [2018-04-20 15:18:42,84] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprep_align_inputs:NA:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'prep_align_inputs' 'cwl' 'sentinel_runtime=cores,2,ram,4096' 'sentinel_parallel=single-single' 'sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split' 'sentinel_inputs=alignment_rec:record'[0m | |
| [2018-04-20 15:18:42,85] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprep_align_inputs:NA:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-alignment/shard-0/wf-alignment.cwl/150711af-1057-4268-b49e-8c2fa3553ebd/call-prep_align_inputs/execution/script | |
| [2018-04-20 15:18:42,85] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprep_align_inputs:NA:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-alignment/shard-2/wf-alignment.cwl/559b1695-f115-4008-b14e-a7ba4d488314/call-prep_align_inputs/execution/script | |
| [2018-04-20 15:18:42,85] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprep_align_inputs:NA:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'prep_align_inputs' 'cwl' 'sentinel_runtime=cores,2,ram,4096' 'sentinel_parallel=single-single' 'sentinel_outputs=process_alignment_rec:files;config__algorithm__quality_format;align_split' 'sentinel_inputs=alignment_rec:record'[0m | |
| [2018-04-20 15:18:42,86] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprep_align_inputs:NA:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-alignment/shard-1/wf-alignment.cwl/b07cdb7e-f4e7-4c47-ab9a-bd6756d18b92/call-prep_align_inputs/execution/script | |
| [2018-04-20 15:18:44,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:2:1]: job id: 16082 | |
| [2018-04-20 15:18:44,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:1:1]: job id: 16078 | |
| [2018-04-20 15:18:44,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:0:1]: job id: 16083 | |
| [2018-04-20 15:18:44,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprep_align_inputs:NA:1]: job id: 16288 | |
| [2018-04-20 15:18:44,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprep_align_inputs:NA:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:44,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:2:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:44,17] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:1:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:44,18] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprep_align_inputs:NA:1]: job id: 16280 | |
| [2018-04-20 15:18:44,18] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprep_align_inputs:NA:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:44,19] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprep_align_inputs:NA:1]: job id: 16282 | |
| [2018-04-20 15:18:44,19] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:0:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:44,19] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprep_align_inputs:NA:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:47,79] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:0:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:18:49,65] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprep_align_inputs:NA:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:18:50,36] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprep_align_inputs:NA:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:18:50,51] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprep_align_inputs:NA:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:18:50,95] [info] b07cdb7e-f4e7-4c47-ab9a-bd6756d18b92-SubWorkflowActor-SubWorkflow-alignment:1:1 [[38;5;2mb07cdb7e[0m]: Starting process_alignment | |
| [2018-04-20 15:18:51,58] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:2:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:18:51,82] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprocess_alignment:NA:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:51,85] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprocess_alignment:NA:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'process_alignment' 'cwl' 'sentinel_runtime=cores,2,ram,4096' 'sentinel_parallel=single-single' 'sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr' 'sentinel_inputs=alignment_rec:record,process_alignment_rec:record'[0m | |
| [2018-04-20 15:18:51,86] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprocess_alignment:NA:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-alignment/shard-1/wf-alignment.cwl/b07cdb7e-f4e7-4c47-ab9a-bd6756d18b92/call-process_alignment/execution/script | |
| [2018-04-20 15:18:51,97] [info] 559b1695-f115-4008-b14e-a7ba4d488314-SubWorkflowActor-SubWorkflow-alignment:2:1 [[38;5;2m559b1695[0m]: Starting process_alignment | |
| [2018-04-20 15:18:51,97] [info] 150711af-1057-4268-b49e-8c2fa3553ebd-SubWorkflowActor-SubWorkflow-alignment:0:1 [[38;5;2m150711af[0m]: Starting process_alignment | |
| [2018-04-20 15:18:52,81] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprocess_alignment:NA:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:52,82] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprocess_alignment:NA:1]: Unrecognized runtime attribute keys: memoryMax, tmpDirMin, cpu, cpuMax, cpuMin, tmpDirMax, outDirMin, memoryMin, outDirMax, memory | |
| [2018-04-20 15:18:52,83] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprocess_alignment:NA:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'process_alignment' 'cwl' 'sentinel_runtime=cores,2,ram,4096' 'sentinel_parallel=single-single' 'sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr' 'sentinel_inputs=alignment_rec:record,process_alignment_rec:record'[0m | |
| [2018-04-20 15:18:52,83] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprocess_alignment:NA:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-alignment/shard-0/wf-alignment.cwl/150711af-1057-4268-b49e-8c2fa3553ebd/call-process_alignment/execution/script | |
| [2018-04-20 15:18:52,84] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprocess_alignment:NA:1]: [38;5;5m'bcbio_nextgen.py' 'runfn' 'process_alignment' 'cwl' 'sentinel_runtime=cores,2,ram,4096' 'sentinel_parallel=single-single' 'sentinel_outputs=work_bam,align_bam,hla__fastq,work_bam_plus__disc,work_bam_plus__sr' 'sentinel_inputs=alignment_rec:record,process_alignment_rec:record'[0m | |
| [2018-04-20 15:18:52,84] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprocess_alignment:NA:1]: executing: /usr/bin/env bash /home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-alignment/shard-2/wf-alignment.cwl/559b1695-f115-4008-b14e-a7ba4d488314/call-process_alignment/execution/script | |
| [2018-04-20 15:18:53,59] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb349aa40[0mprep_samples:1:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:18:54,11] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprocess_alignment:NA:1]: job id: 17024 | |
| [2018-04-20 15:18:54,12] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprocess_alignment:NA:1]: job id: 17107 | |
| [2018-04-20 15:18:54,12] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprocess_alignment:NA:1]: job id: 17110 | |
| [2018-04-20 15:18:54,12] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprocess_alignment:NA:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:54,12] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprocess_alignment:NA:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:54,12] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprocess_alignment:NA:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-04-20 15:18:59,04] [[38;5;220mwarn[0m] JobExecutionTokenDispenser - High load alert. Freeze token distribution. | |
| [2018-04-20 15:18:59,83] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m559b1695[0mprocess_alignment:NA:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:19:00,15] [info] 559b1695-f115-4008-b14e-a7ba4d488314-SubWorkflowActor-SubWorkflow-alignment:2:1 [[38;5;2m559b1695[0m]: Workflow wf-alignment.cwl complete. Final Outputs: | |
| { | |
| "wf-alignment.cwl.align_bam": "\"/home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-alignment/shard-2/wf-alignment.cwl/559b1695-f115-4008-b14e-a7ba4d488314/call-process_alignment/execution/prealign/Test1/Test1-prealign.bam\"", | |
| "wf-alignment.cwl.work_bam_plus__sr": null, | |
| "wf-alignment.cwl.hla__fastq": null, | |
| "wf-alignment.cwl.work_bam_plus__disc": null | |
| } | |
| [2018-04-20 15:19:00,87] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m150711af[0mprocess_alignment:NA:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:19:01,15] [info] 150711af-1057-4268-b49e-8c2fa3553ebd-SubWorkflowActor-SubWorkflow-alignment:0:1 [[38;5;2m150711af[0m]: Workflow wf-alignment.cwl complete. Final Outputs: | |
| { | |
| "wf-alignment.cwl.align_bam": null, | |
| "wf-alignment.cwl.work_bam_plus__sr": null, | |
| "wf-alignment.cwl.hla__fastq": null, | |
| "wf-alignment.cwl.work_bam_plus__disc": null | |
| } | |
| [2018-04-20 15:19:05,30] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2mb07cdb7e[0mprocess_alignment:NA:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-04-20 15:19:06,25] [info] b07cdb7e-f4e7-4c47-ab9a-bd6756d18b92-SubWorkflowActor-SubWorkflow-alignment:1:1 [[38;5;2mb07cdb7e[0m]: Workflow wf-alignment.cwl complete. Final Outputs: | |
| { | |
| "wf-alignment.cwl.work_bam_plus__sr": null, | |
| "wf-alignment.cwl.align_bam": "\"/home/chapmanb/drive/work/cwl/test_bcbio_cwl/somatic/cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/call-alignment/shard-1/wf-alignment.cwl/b07cdb7e-f4e7-4c47-ab9a-bd6756d18b92/call-process_alignment/execution/align/Test2/Test2-sort.bam\"", | |
| "wf-alignment.cwl.hla__fastq": null, | |
| "wf-alignment.cwl.work_bam_plus__disc": null | |
| } | |
| [2018-04-20 15:19:09,28] [info] WorkflowExecutionActor-b349aa40-9376-47ab-a345-86745a8545b6 [[38;5;2mb349aa40[0m]: Starting postprocess_alignment_to_rec | |
| ^CTraceback (most recent call last): | |
| File "/usr/local/bin/bcbio_vm.py", line 4, in <module> | |
| __import__('pkg_resources').run_script('bcbio-nextgen-vm==0.1.0a0', 'bcbio_vm.py') | |
| File "/usr/local/share/bcbio-vm/lib/python2.7/site-packages/pkg_resources/__init__.py", line 748, in run_script | |
| self.require(requires)[0].run_script(script_name, ns) | |
| File "/usr/local/share/bcbio-vm/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1517, in run_script | |
| exec(code, namespace, namespace) | |
| File "/usr/local/share/bcbio-vm/lib/python2.7/site-packages/bcbio_nextgen_vm-0.1.0a0-py2.7.egg/EGG-INFO/scripts/bcbio_vm.py", line 335, in <module> | |
| args.func(args) | |
| File "/usr/local/share/bcbio-vm/lib/python2.7/site-packages/bcbio_nextgen-1.1.0a0-py2.7.egg/bcbio/cwl/tool.py", line 224, in run | |
| _TOOLS[args.tool](args) | |
| File "/usr/local/share/bcbio-vm/lib/python2.7/site-packages/bcbio_nextgen-1.1.0a0-py2.7.egg/bcbio/cwl/tool.py", line 146, in _run_cromwell | |
| _run_tool(cmd, not args.no_container, work_dir, log_file) | |
| File "/usr/local/share/bcbio-vm/lib/python2.7/site-packages/bcbio_nextgen-1.1.0a0-py2.7.egg/bcbio/cwl/tool.py", line 38, in _run_tool | |
| subprocess.check_call(cmd, shell=True) | |
| File "/usr/local/share/bcbio-vm/lib/python2.7/subprocess.py", line 181, in check_call | |
| retcode = call(*popenargs, **kwargs) | |
| File "/usr/local/share/bcbio-vm/lib/python2.7/subprocess.py", line 168, in call | |
| return Popen(*popenargs, **kwargs).wait() | |
| File "/usr/local/share/bcbio-vm/lib/python2.7/subprocess.py", line 1077, in wait | |
| pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0) | |
| File "/usr/local/share/bcbio-vm/lib/python2.7/subprocess.py", line 121, in _eintr_retry_call | |
| return func(*args) | |
| KeyboardInterrupt | |
| $ tree cromwell_work/cromwell-executions/main-somatic.cwl/b349aa40-9376-47ab-a345-86745a8545b6/ | |
| ├── [01;34mcall-alignment[00m | |
| │ ├── [01;34mshard-0[00m | |
| │ │ └── [01;34mwf-alignment.cwl[00m | |
| │ │ └── [01;34m150711af-1057-4268-b49e-8c2fa3553ebd[00m | |
| │ │ ├── [01;34mcall-prep_align_inputs[00m | |
| │ │ │ ├── [01;34mexecution[00m | |
| │ │ │ │ ├── cwl.inputs.json | |
| │ │ │ │ ├── cwl.output.json | |
| │ │ │ │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ │ │ │ ├── cromwell_glob_control_file | |
| │ │ │ │ │ └── cwl.output.json | |
| │ │ │ │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ │ │ │ ├── [01;34mlog[00m | |
| │ │ │ │ │ ├── bcbio-nextgen-commands.log | |
| │ │ │ │ │ ├── bcbio-nextgen-debug.log | |
| │ │ │ │ │ └── bcbio-nextgen.log | |
| │ │ │ │ ├── rc | |
| │ │ │ │ ├── script | |
| │ │ │ │ ├── script.background | |
| │ │ │ │ ├── script.submit | |
| │ │ │ │ ├── stderr | |
| │ │ │ │ ├── stderr.background | |
| │ │ │ │ ├── stdout | |
| │ │ │ │ ├── stdout.background | |
| │ │ │ │ └── wdl.output.process_alignment_rec.txt | |
| │ │ │ ├── [01;34minputs[00m | |
| │ │ │ │ └── [01;34m583512350[00m | |
| │ │ │ │ ├── hg19.dict | |
| │ │ │ │ ├── hg19.fa | |
| │ │ │ │ └── hg19.fa.fai | |
| │ │ │ └── [34;42mtmp.cfda7822[00m | |
| │ │ └── [01;34mcall-process_alignment[00m | |
| │ │ ├── [01;34mexecution[00m | |
| │ │ │ ├── cwl.inputs.json | |
| │ │ │ ├── cwl.output.json | |
| │ │ │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ │ │ ├── cromwell_glob_control_file | |
| │ │ │ │ └── cwl.output.json | |
| │ │ │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ │ │ ├── [01;34mlog[00m | |
| │ │ │ │ ├── bcbio-nextgen-commands.log | |
| │ │ │ │ ├── bcbio-nextgen-debug.log | |
| │ │ │ │ └── bcbio-nextgen.log | |
| │ │ │ ├── rc | |
| │ │ │ ├── script | |
| │ │ │ ├── script.background | |
| │ │ │ ├── script.submit | |
| │ │ │ ├── stderr | |
| │ │ │ ├── stderr.background | |
| │ │ │ ├── stdout | |
| │ │ │ ├── stdout.background | |
| │ │ │ ├── wdl.output.align_bam.txt | |
| │ │ │ ├── wdl.output.hla__fastq.txt | |
| │ │ │ ├── wdl.output.work_bam_plus__disc.txt | |
| │ │ │ ├── wdl.output.work_bam_plus__sr.txt | |
| │ │ │ └── wdl.output.work_bam.txt | |
| │ │ ├── [01;34minputs[00m | |
| │ │ │ └── [01;34m583512350[00m | |
| │ │ │ ├── hg19.dict | |
| │ │ │ ├── hg19.fa | |
| │ │ │ └── hg19.fa.fai | |
| │ │ └── [34;42mtmp.2925ae15[00m | |
| │ ├── [01;34mshard-1[00m | |
| │ │ └── [01;34mwf-alignment.cwl[00m | |
| │ │ └── [01;34mb07cdb7e-f4e7-4c47-ab9a-bd6756d18b92[00m | |
| │ │ ├── [01;34mcall-prep_align_inputs[00m | |
| │ │ │ ├── [01;34mexecution[00m | |
| │ │ │ │ ├── [01;34malign_prep[00m | |
| │ │ │ │ │ ├── [01;31mTest2_7_100326_FC6107FAAXX_1.fq.gz[00m | |
| │ │ │ │ │ ├── Test2_7_100326_FC6107FAAXX_1.fq.gz.gbi | |
| │ │ │ │ │ ├── [01;31mTest2_7_100326_FC6107FAAXX_2.fq.gz[00m | |
| │ │ │ │ │ └── Test2_7_100326_FC6107FAAXX_2.fq.gz.gbi | |
| │ │ │ │ ├── [01;34mbcbiotx[00m | |
| │ │ │ │ ├── cwl.inputs.json | |
| │ │ │ │ ├── cwl.output.json | |
| │ │ │ │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ │ │ │ ├── cromwell_glob_control_file | |
| │ │ │ │ │ └── cwl.output.json | |
| │ │ │ │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ │ │ │ ├── [01;34mlog[00m | |
| │ │ │ │ │ ├── bcbio-nextgen-commands.log | |
| │ │ │ │ │ ├── bcbio-nextgen-debug.log | |
| │ │ │ │ │ └── bcbio-nextgen.log | |
| │ │ │ │ ├── rc | |
| │ │ │ │ ├── script | |
| │ │ │ │ ├── script.background | |
| │ │ │ │ ├── script.submit | |
| │ │ │ │ ├── stderr | |
| │ │ │ │ ├── stderr.background | |
| │ │ │ │ ├── stdout | |
| │ │ │ │ ├── stdout.background | |
| │ │ │ │ └── wdl.output.process_alignment_rec.txt | |
| │ │ │ ├── [01;34minputs[00m | |
| │ │ │ │ └── [01;34m583512350[00m | |
| │ │ │ │ ├── hg19.dict | |
| │ │ │ │ ├── hg19.fa | |
| │ │ │ │ └── hg19.fa.fai | |
| │ │ │ └── [34;42mtmp.6ec93f1b[00m | |
| │ │ └── [01;34mcall-process_alignment[00m | |
| │ │ ├── [01;34mexecution[00m | |
| │ │ │ ├── [01;34malign[00m | |
| │ │ │ │ └── [01;34mTest2[00m | |
| │ │ │ │ ├── Test2-sort.bam | |
| │ │ │ │ └── Test2-sort.bam.bai | |
| │ │ │ ├── [01;34mbcbiotx[00m | |
| │ │ │ ├── cwl.inputs.json | |
| │ │ │ ├── cwl.output.json | |
| │ │ │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ │ │ ├── cromwell_glob_control_file | |
| │ │ │ │ └── cwl.output.json | |
| │ │ │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ │ │ ├── [01;34mlog[00m | |
| │ │ │ │ ├── bcbio-nextgen-commands.log | |
| │ │ │ │ ├── bcbio-nextgen-debug.log | |
| │ │ │ │ └── bcbio-nextgen.log | |
| │ │ │ ├── rc | |
| │ │ │ ├── script | |
| │ │ │ ├── script.background | |
| │ │ │ ├── script.submit | |
| │ │ │ ├── stderr | |
| │ │ │ ├── stderr.background | |
| │ │ │ ├── stdout | |
| │ │ │ ├── stdout.background | |
| │ │ │ ├── wdl.output.align_bam.txt | |
| │ │ │ ├── wdl.output.hla__fastq.txt | |
| │ │ │ ├── wdl.output.work_bam_plus__disc.txt | |
| │ │ │ ├── wdl.output.work_bam_plus__sr.txt | |
| │ │ │ └── wdl.output.work_bam.txt | |
| │ │ ├── [01;34minputs[00m | |
| │ │ │ ├── [01;34m2122719215[00m | |
| │ │ │ │ ├── [01;31mTest2_7_100326_FC6107FAAXX_1.fq.gz[00m | |
| │ │ │ │ ├── Test2_7_100326_FC6107FAAXX_1.fq.gz.gbi | |
| │ │ │ │ ├── [01;31mTest2_7_100326_FC6107FAAXX_2.fq.gz[00m | |
| │ │ │ │ └── Test2_7_100326_FC6107FAAXX_2.fq.gz.gbi | |
| │ │ │ └── [01;34m583512350[00m | |
| │ │ │ ├── hg19.dict | |
| │ │ │ ├── hg19.fa | |
| │ │ │ └── hg19.fa.fai | |
| │ │ └── [34;42mtmp.c39bc0a5[00m | |
| │ └── [01;34mshard-2[00m | |
| │ └── [01;34mwf-alignment.cwl[00m | |
| │ └── [01;34m559b1695-f115-4008-b14e-a7ba4d488314[00m | |
| │ ├── [01;34mcall-prep_align_inputs[00m | |
| │ │ ├── [01;34mexecution[00m | |
| │ │ │ ├── cwl.inputs.json | |
| │ │ │ ├── cwl.output.json | |
| │ │ │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ │ │ ├── cromwell_glob_control_file | |
| │ │ │ │ └── cwl.output.json | |
| │ │ │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ │ │ ├── [01;34mlog[00m | |
| │ │ │ │ ├── bcbio-nextgen-commands.log | |
| │ │ │ │ ├── bcbio-nextgen-debug.log | |
| │ │ │ │ └── bcbio-nextgen.log | |
| │ │ │ ├── rc | |
| │ │ │ ├── script | |
| │ │ │ ├── script.background | |
| │ │ │ ├── script.submit | |
| │ │ │ ├── stderr | |
| │ │ │ ├── stderr.background | |
| │ │ │ ├── stdout | |
| │ │ │ ├── stdout.background | |
| │ │ │ └── wdl.output.process_alignment_rec.txt | |
| │ │ ├── [01;34minputs[00m | |
| │ │ │ └── [01;34m583512350[00m | |
| │ │ │ ├── hg19.dict | |
| │ │ │ ├── hg19.fa | |
| │ │ │ └── hg19.fa.fai | |
| │ │ └── [34;42mtmp.cabbe361[00m | |
| │ └── [01;34mcall-process_alignment[00m | |
| │ ├── [01;34mexecution[00m | |
| │ │ ├── [01;34mbcbiotx[00m | |
| │ │ ├── cwl.inputs.json | |
| │ │ ├── cwl.output.json | |
| │ │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ │ ├── cromwell_glob_control_file | |
| │ │ │ └── cwl.output.json | |
| │ │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ │ ├── [01;34mlog[00m | |
| │ │ │ ├── bcbio-nextgen-commands.log | |
| │ │ │ ├── bcbio-nextgen-debug.log | |
| │ │ │ └── bcbio-nextgen.log | |
| │ │ ├── [01;34mprealign[00m | |
| │ │ │ └── [01;34mTest1[00m | |
| │ │ │ ├── Test1-prealign.bam | |
| │ │ │ └── Test1-prealign.bam.bai | |
| │ │ ├── rc | |
| │ │ ├── script | |
| │ │ ├── script.background | |
| │ │ ├── script.submit | |
| │ │ ├── stderr | |
| │ │ ├── stderr.background | |
| │ │ ├── stdout | |
| │ │ ├── stdout.background | |
| │ │ ├── wdl.output.align_bam.txt | |
| │ │ ├── wdl.output.hla__fastq.txt | |
| │ │ ├── wdl.output.work_bam_plus__disc.txt | |
| │ │ ├── wdl.output.work_bam_plus__sr.txt | |
| │ │ └── wdl.output.work_bam.txt | |
| │ ├── [01;34minputs[00m | |
| │ │ ├── [01;34m1635740323[00m | |
| │ │ │ └── 6_100326_FC6107FAAXX.bam | |
| │ │ └── [01;34m583512350[00m | |
| │ │ ├── hg19.dict | |
| │ │ ├── hg19.fa | |
| │ │ └── hg19.fa.fai | |
| │ └── [34;42mtmp.f4282ba2[00m | |
| ├── [01;34mcall-alignment_to_rec[00m | |
| │ ├── [01;34mexecution[00m | |
| │ │ ├── cwl.inputs.json | |
| │ │ ├── cwl.output.json | |
| │ │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ │ ├── cromwell_glob_control_file | |
| │ │ │ └── cwl.output.json | |
| │ │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ │ ├── [01;34mlog[00m | |
| │ │ │ ├── bcbio-nextgen-commands.log | |
| │ │ │ ├── bcbio-nextgen-debug.log | |
| │ │ │ └── bcbio-nextgen.log | |
| │ │ ├── rc | |
| │ │ ├── script | |
| │ │ ├── script.background | |
| │ │ ├── script.submit | |
| │ │ ├── stderr | |
| │ │ ├── stderr.background | |
| │ │ ├── stdout | |
| │ │ ├── stdout.background | |
| │ │ └── wdl.output.alignment_rec.txt | |
| │ ├── [01;34minputs[00m | |
| │ │ └── [01;34m222597375[00m | |
| │ │ ├── hg19.dict | |
| │ │ ├── hg19.fa | |
| │ │ └── hg19.fa.fai | |
| │ └── [34;42mtmp.e59be950[00m | |
| ├── [01;34mcall-prep_samples[00m | |
| │ ├── [01;34mshard-0[00m | |
| │ │ ├── [01;34mexecution[00m | |
| │ │ │ ├── cwl.inputs.json | |
| │ │ │ ├── cwl.output.json | |
| │ │ │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ │ │ ├── cromwell_glob_control_file | |
| │ │ │ │ └── cwl.output.json | |
| │ │ │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ │ │ ├── [01;34mlog[00m | |
| │ │ │ │ ├── bcbio-nextgen-commands.log | |
| │ │ │ │ ├── bcbio-nextgen-debug.log | |
| │ │ │ │ └── bcbio-nextgen.log | |
| │ │ │ ├── rc | |
| │ │ │ ├── script | |
| │ │ │ ├── script.background | |
| │ │ │ ├── script.submit | |
| │ │ │ ├── stderr | |
| │ │ │ ├── stderr.background | |
| │ │ │ ├── stdout | |
| │ │ │ ├── stdout.background | |
| │ │ │ ├── wdl.output.config__algorithm__coverage_merged.txt | |
| │ │ │ ├── wdl.output.config__algorithm__coverage_orig.txt | |
| │ │ │ ├── wdl.output.config__algorithm__coverage.txt | |
| │ │ │ ├── wdl.output.config__algorithm__seq2c_bed_ready.txt | |
| │ │ │ ├── wdl.output.config__algorithm__variant_regions_merged.txt | |
| │ │ │ ├── wdl.output.config__algorithm__variant_regions_orig.txt | |
| │ │ │ └── wdl.output.config__algorithm__variant_regions.txt | |
| │ │ ├── [01;34minputs[00m | |
| │ │ │ └── [01;34m-577677000[00m | |
| │ │ │ ├── hg19.dict | |
| │ │ │ ├── hg19.fa | |
| │ │ │ └── hg19.fa.fai | |
| │ │ └── [34;42mtmp.6f9b2b6a[00m | |
| │ ├── [01;34mshard-1[00m | |
| │ │ ├── [01;34mexecution[00m | |
| │ │ │ ├── [01;34mbcbiotx[00m | |
| │ │ │ ├── [01;34mbedprep[00m | |
| │ │ │ │ ├── cleaned-variant_regions-bam.bed | |
| │ │ │ │ ├── [01;31mcleaned-variant_regions-bam.bed.gz[00m | |
| │ │ │ │ ├── cleaned-variant_regions-bam.bed.gz.tbi | |
| │ │ │ │ ├── cleaned-variant_regions-bam-merged.bed | |
| │ │ │ │ ├── [01;31mcleaned-variant_regions-bam-merged.bed.gz[00m | |
| │ │ │ │ ├── cleaned-variant_regions-bam-merged.bed.gz.tbi | |
| │ │ │ │ ├── cov-coverage_transcripts-bam.bed | |
| │ │ │ │ ├── [01;31mcov-coverage_transcripts-bam.bed.gz[00m | |
| │ │ │ │ ├── cov-coverage_transcripts-bam.bed.gz.tbi | |
| │ │ │ │ ├── cov-coverage_transcripts-bam-merged.bed | |
| │ │ │ │ ├── [01;31mcov-coverage_transcripts-bam-merged.bed.gz[00m | |
| │ │ │ │ ├── cov-coverage_transcripts-bam-merged.bed.gz.tbi | |
| │ │ │ │ ├── svregions-cleaned-variant_regions-bam.bed | |
| │ │ │ │ ├── [01;31msvregions-cleaned-variant_regions-bam.bed.gz[00m | |
| │ │ │ │ └── svregions-cleaned-variant_regions-bam.bed.gz.tbi | |
| │ │ │ ├── cwl.inputs.json | |
| │ │ │ ├── cwl.output.json | |
| │ │ │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ │ │ ├── cromwell_glob_control_file | |
| │ │ │ │ └── cwl.output.json | |
| │ │ │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ │ │ ├── [01;34mlog[00m | |
| │ │ │ │ ├── bcbio-nextgen-commands.log | |
| │ │ │ │ ├── bcbio-nextgen-debug.log | |
| │ │ │ │ └── bcbio-nextgen.log | |
| │ │ │ ├── rc | |
| │ │ │ ├── script | |
| │ │ │ ├── script.background | |
| │ │ │ ├── script.submit | |
| │ │ │ ├── stderr | |
| │ │ │ ├── stderr.background | |
| │ │ │ ├── stdout | |
| │ │ │ ├── stdout.background | |
| │ │ │ ├── wdl.output.config__algorithm__coverage_merged.txt | |
| │ │ │ ├── wdl.output.config__algorithm__coverage_orig.txt | |
| │ │ │ ├── wdl.output.config__algorithm__coverage.txt | |
| │ │ │ ├── wdl.output.config__algorithm__seq2c_bed_ready.txt | |
| │ │ │ ├── wdl.output.config__algorithm__variant_regions_merged.txt | |
| │ │ │ ├── wdl.output.config__algorithm__variant_regions_orig.txt | |
| │ │ │ └── wdl.output.config__algorithm__variant_regions.txt | |
| │ │ ├── [01;34minputs[00m | |
| │ │ │ └── [01;34m-577677000[00m | |
| │ │ │ ├── hg19.dict | |
| │ │ │ ├── hg19.fa | |
| │ │ │ └── hg19.fa.fai | |
| │ │ └── [34;42mtmp.0858dfd9[00m | |
| │ └── [01;34mshard-2[00m | |
| │ ├── [01;34mexecution[00m | |
| │ │ ├── [01;34mbcbiotx[00m | |
| │ │ ├── [01;34mbedprep[00m | |
| │ │ │ ├── cleaned-variant_regions-bam.bed | |
| │ │ │ ├── [01;31mcleaned-variant_regions-bam.bed.gz[00m | |
| │ │ │ ├── cleaned-variant_regions-bam.bed.gz.tbi | |
| │ │ │ ├── cleaned-variant_regions-bam-merged.bed | |
| │ │ │ ├── [01;31mcleaned-variant_regions-bam-merged.bed.gz[00m | |
| │ │ │ ├── cleaned-variant_regions-bam-merged.bed.gz.tbi | |
| │ │ │ ├── svregions-cleaned-variant_regions-bam.bed | |
| │ │ │ ├── [01;31msvregions-cleaned-variant_regions-bam.bed.gz[00m | |
| │ │ │ └── svregions-cleaned-variant_regions-bam.bed.gz.tbi | |
| │ │ ├── cwl.inputs.json | |
| │ │ ├── cwl.output.json | |
| │ │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ │ ├── cromwell_glob_control_file | |
| │ │ │ └── cwl.output.json | |
| │ │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ │ ├── [01;34mlog[00m | |
| │ │ │ ├── bcbio-nextgen-commands.log | |
| │ │ │ ├── bcbio-nextgen-debug.log | |
| │ │ │ └── bcbio-nextgen.log | |
| │ │ ├── rc | |
| │ │ ├── script | |
| │ │ ├── script.background | |
| │ │ ├── script.submit | |
| │ │ ├── stderr | |
| │ │ ├── stderr.background | |
| │ │ ├── stdout | |
| │ │ ├── stdout.background | |
| │ │ ├── wdl.output.config__algorithm__coverage_merged.txt | |
| │ │ ├── wdl.output.config__algorithm__coverage_orig.txt | |
| │ │ ├── wdl.output.config__algorithm__coverage.txt | |
| │ │ ├── wdl.output.config__algorithm__seq2c_bed_ready.txt | |
| │ │ ├── wdl.output.config__algorithm__variant_regions_merged.txt | |
| │ │ ├── wdl.output.config__algorithm__variant_regions_orig.txt | |
| │ │ └── wdl.output.config__algorithm__variant_regions.txt | |
| │ ├── [01;34minputs[00m | |
| │ │ └── [01;34m-577677000[00m | |
| │ │ ├── hg19.dict | |
| │ │ ├── hg19.fa | |
| │ │ └── hg19.fa.fai | |
| │ └── [34;42mtmp.f37f9e45[00m | |
| └── [01;34mcall-prep_samples_to_rec[00m | |
| ├── [01;34mexecution[00m | |
| │ ├── cwl.inputs.json | |
| │ ├── cwl.output.json | |
| │ ├── [01;34mglob-b34dfc006a981a93d6da067cf50036fe[00m | |
| │ │ ├── cromwell_glob_control_file | |
| │ │ └── cwl.output.json | |
| │ ├── glob-b34dfc006a981a93d6da067cf50036fe.list | |
| │ ├── [01;34mlog[00m | |
| │ │ ├── bcbio-nextgen-commands.log | |
| │ │ ├── bcbio-nextgen-debug.log | |
| │ │ └── bcbio-nextgen.log | |
| │ ├── rc | |
| │ ├── script | |
| │ ├── script.background | |
| │ ├── script.submit | |
| │ ├── stderr | |
| │ ├── stderr.background | |
| │ ├── stdout | |
| │ ├── stdout.background | |
| │ └── wdl.output.prep_samples_rec.txt | |
| ├── [01;34minputs[00m | |
| │ └── [01;34m222597375[00m | |
| │ ├── hg19.dict | |
| │ ├── hg19.fa | |
| │ └── hg19.fa.fai | |
| └── [34;42mtmp.145caa17[00m | |
| 102 directories, 287 files | |
| Script done on Fri 20 Apr 2018 03:22:04 PM EDT |
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