[2024-04-26 06:18:19,86] [info] Running with database db.url = jdbc:hsqldb:file:cromwell-executions/cromwell-db/cromwell-db; shutdown=false; hsqldb.default_table_type=cached;hsqldb.tx=mvcc; hsqldb.result_max_memory_rows=10000; hsqldb.large_data=true; hsqldb.applog=1; hsqldb.lob_compressed=true; hsqldb.script_format=3 [2024-04-26 06:18:20,18] [info] dataFileCache open start [2024-04-26 06:18:20,20] [info] dataFileCache open end [2024-04-26 06:18:20,28] [info] checkpointClose start [2024-04-26 06:18:20,28] [info] checkpointClose synched [2024-04-26 06:18:20,30] [info] checkpointClose script done [2024-04-26 06:18:20,30] [info] dataFileCache commit start [2024-04-26 06:18:20,32] [info] dataFileCache commit end [2024-04-26 06:18:20,34] [info] checkpointClose end [2024-04-26 06:18:23,42] [info] Checkpoint start [2024-04-26 06:18:23,43] [info] checkpointClose start [2024-04-26 06:18:23,43] [info] checkpointClose synched [2024-04-26 06:18:23,45] [info] checkpointClose script done [2024-04-26 06:18:23,45] [info] dataFileCache commit start [2024-04-26 06:18:23,45] [info] dataFileCache commit end [2024-04-26 06:18:23,46] [info] checkpointClose end [2024-04-26 06:18:23,46] [info] Checkpoint end - txts: 14675 [2024-04-26 06:18:23,51] [info] Checkpoint start [2024-04-26 06:18:23,51] [info] checkpointClose start [2024-04-26 06:18:23,51] [info] checkpointClose synched [2024-04-26 06:18:23,52] [info] checkpointClose script done [2024-04-26 06:18:23,53] [info] dataFileCache commit start [2024-04-26 06:18:23,54] [info] dataFileCache commit end [2024-04-26 06:18:23,55] [info] checkpointClose end [2024-04-26 06:18:23,55] [info] Checkpoint end - txts: 14691 [2024-04-26 06:18:23,55] [info] Checkpoint start [2024-04-26 06:18:23,55] [info] checkpointClose start [2024-04-26 06:18:23,55] [info] checkpointClose synched [2024-04-26 06:18:23,56] [info] checkpointClose script done [2024-04-26 06:18:23,56] [info] dataFileCache commit start [2024-04-26 06:18:23,57] [info] dataFileCache commit end [2024-04-26 06:18:23,58] [info] checkpointClose end [2024-04-26 06:18:23,58] [info] Checkpoint end - txts: 14693 [2024-04-26 06:18:24,72] [info] Checkpoint start [2024-04-26 06:18:24,72] [info] checkpointClose start [2024-04-26 06:18:24,72] [info] checkpointClose synched [2024-04-26 06:18:24,73] [info] checkpointClose script done [2024-04-26 06:18:24,73] [info] dataFileCache commit start [2024-04-26 06:18:24,73] [info] dataFileCache commit end [2024-04-26 06:18:24,74] [info] checkpointClose end [2024-04-26 06:18:24,74] [info] Checkpoint end - txts: 14716 [2024-04-26 06:18:24,74] [info] Checkpoint start [2024-04-26 06:18:24,74] [info] checkpointClose start [2024-04-26 06:18:24,75] [info] checkpointClose synched [2024-04-26 06:18:24,75] [info] checkpointClose script done [2024-04-26 06:18:24,75] [info] dataFileCache commit start [2024-04-26 06:18:24,76] [info] dataFileCache commit end [2024-04-26 06:18:24,77] [info] checkpointClose end [2024-04-26 06:18:24,77] [info] Checkpoint end - txts: 14718 [2024-04-26 06:18:24,83] [info] Checkpoint start [2024-04-26 06:18:24,83] [info] checkpointClose start [2024-04-26 06:18:24,83] [info] checkpointClose synched [2024-04-26 06:18:24,84] [info] checkpointClose script done [2024-04-26 06:18:24,84] [info] dataFileCache commit start [2024-04-26 06:18:24,85] [info] dataFileCache commit end [2024-04-26 06:18:24,86] [info] checkpointClose end [2024-04-26 06:18:24,86] [info] Checkpoint end - txts: 14720 [2024-04-26 06:18:24,86] [info] Checkpoint start [2024-04-26 06:18:24,86] [info] checkpointClose start [2024-04-26 06:18:24,87] [info] checkpointClose synched [2024-04-26 06:18:24,87] [info] checkpointClose script done [2024-04-26 06:18:24,87] [info] dataFileCache commit start [2024-04-26 06:18:24,89] [info] dataFileCache commit end [2024-04-26 06:18:24,90] [info] checkpointClose end [2024-04-26 06:18:24,90] [info] Checkpoint end - txts: 14727 [2024-04-26 06:18:24,90] [info] Checkpoint start [2024-04-26 06:18:24,90] [info] checkpointClose start [2024-04-26 06:18:24,90] [info] checkpointClose synched [2024-04-26 06:18:24,91] [info] checkpointClose script done [2024-04-26 06:18:24,91] [info] dataFileCache commit start [2024-04-26 06:18:24,91] [info] dataFileCache commit end [2024-04-26 06:18:24,92] [info] checkpointClose end [2024-04-26 06:18:24,92] [info] Checkpoint end - txts: 14729 [2024-04-26 06:18:24,92] [info] Checkpoint start [2024-04-26 06:18:24,92] [info] checkpointClose start [2024-04-26 06:18:24,93] [info] checkpointClose synched [2024-04-26 06:18:24,93] [info] checkpointClose script done [2024-04-26 06:18:24,93] [info] dataFileCache commit start [2024-04-26 06:18:24,94] [info] dataFileCache commit end [2024-04-26 06:18:24,95] [info] checkpointClose end [2024-04-26 06:18:24,95] [info] Checkpoint end - txts: 14731 [2024-04-26 06:18:24,96] [info] Running with database db.url = jdbc:hsqldb:file:cromwell-executions/cromwell-db/cromwell-db; shutdown=false; hsqldb.default_table_type=cached;hsqldb.tx=mvcc; hsqldb.result_max_memory_rows=10000; hsqldb.large_data=true; hsqldb.applog=1; hsqldb.lob_compressed=true; hsqldb.script_format=3 [2024-04-26 06:18:24,98] [info] Checkpoint start [2024-04-26 06:18:24,98] [info] checkpointClose start [2024-04-26 06:18:24,98] [info] checkpointClose synched [2024-04-26 06:18:24,99] [info] checkpointClose script done [2024-04-26 06:18:24,99] [info] dataFileCache commit start [2024-04-26 06:18:25,00] [info] dataFileCache commit end [2024-04-26 06:18:25,01] [info] checkpointClose end [2024-04-26 06:18:25,01] [info] Checkpoint end - txts: 14739 [2024-04-26 06:18:25,02] [info] Checkpoint start [2024-04-26 06:18:25,02] [info] checkpointClose start [2024-04-26 06:18:25,02] [info] checkpointClose synched [2024-04-26 06:18:25,03] [info] checkpointClose script done [2024-04-26 06:18:25,03] [info] dataFileCache commit start [2024-04-26 06:18:25,04] [info] dataFileCache commit end [2024-04-26 06:18:25,05] [info] checkpointClose end [2024-04-26 06:18:25,05] [info] Checkpoint end - txts: 14755 [2024-04-26 06:18:25,05] [info] Checkpoint start [2024-04-26 06:18:25,05] [info] checkpointClose start [2024-04-26 06:18:25,05] [info] checkpointClose synched [2024-04-26 06:18:25,06] [info] checkpointClose script done [2024-04-26 06:18:25,06] [info] dataFileCache commit start [2024-04-26 06:18:25,06] [info] dataFileCache commit end [2024-04-26 06:18:25,07] [info] checkpointClose end [2024-04-26 06:18:25,07] [info] Checkpoint end - txts: 14757 [2024-04-26 06:18:25,23] [info] Checkpoint start [2024-04-26 06:18:25,23] [info] checkpointClose start [2024-04-26 06:18:25,24] [info] checkpointClose synched [2024-04-26 06:18:25,24] [info] checkpointClose script done [2024-04-26 06:18:25,24] [info] dataFileCache commit start [2024-04-26 06:18:25,25] [info] dataFileCache commit end [2024-04-26 06:18:25,26] [info] checkpointClose end [2024-04-26 06:18:25,26] [info] Checkpoint end - txts: 14780 [2024-04-26 06:18:25,26] [info] Checkpoint start [2024-04-26 06:18:25,26] [info] checkpointClose start [2024-04-26 06:18:25,26] [info] checkpointClose synched [2024-04-26 06:18:25,27] [info] checkpointClose script done [2024-04-26 06:18:25,27] [info] dataFileCache commit start [2024-04-26 06:18:25,27] [info] dataFileCache commit end [2024-04-26 06:18:25,28] [info] checkpointClose end [2024-04-26 06:18:25,28] [info] Checkpoint end - txts: 14782 [2024-04-26 06:18:25,29] [info] Checkpoint start [2024-04-26 06:18:25,29] [info] checkpointClose start [2024-04-26 06:18:25,29] [info] checkpointClose synched [2024-04-26 06:18:25,30] [info] checkpointClose script done [2024-04-26 06:18:25,30] [info] dataFileCache commit start [2024-04-26 06:18:25,31] [info] dataFileCache commit end [2024-04-26 06:18:25,32] [info] checkpointClose end [2024-04-26 06:18:25,32] [info] Checkpoint end - txts: 14784 [2024-04-26 06:18:25,32] [info] Checkpoint start [2024-04-26 06:18:25,32] [info] checkpointClose start [2024-04-26 06:18:25,33] [info] checkpointClose synched [2024-04-26 06:18:25,33] [info] checkpointClose script done [2024-04-26 06:18:25,33] [info] dataFileCache commit start [2024-04-26 06:18:25,34] [info] dataFileCache commit end [2024-04-26 06:18:25,35] [info] checkpointClose end [2024-04-26 06:18:25,35] [info] Checkpoint end - txts: 14791 [2024-04-26 06:18:25,36] [info] Checkpoint start [2024-04-26 06:18:25,36] [info] checkpointClose start [2024-04-26 06:18:25,36] [info] checkpointClose synched [2024-04-26 06:18:25,37] [info] checkpointClose script done [2024-04-26 06:18:25,37] [info] dataFileCache commit start [2024-04-26 06:18:25,37] [info] dataFileCache commit end [2024-04-26 06:18:25,38] [info] checkpointClose end [2024-04-26 06:18:25,38] [info] Checkpoint end - txts: 14793 [2024-04-26 06:18:25,38] [info] Checkpoint start [2024-04-26 06:18:25,38] [info] checkpointClose start [2024-04-26 06:18:25,39] [info] checkpointClose synched [2024-04-26 06:18:25,39] [info] checkpointClose script done [2024-04-26 06:18:25,39] [info] dataFileCache commit start [2024-04-26 06:18:25,40] [info] dataFileCache commit end [2024-04-26 06:18:25,41] [info] checkpointClose end [2024-04-26 06:18:25,41] [info] Checkpoint end - txts: 14795 [2024-04-26 06:18:25,56] [info] Slf4jLogger started [2024-04-26 06:18:25,72] [info] Workflow heartbeat configuration: { "cromwellId" : "cromid-3d67e9c", "heartbeatInterval" : "2 minutes", "ttl" : "10 minutes", "failureShutdownDuration" : "5 minutes", "writeBatchSize" : 10000, "writeThreshold" : 10000 } [2024-04-26 06:18:25,77] [info] Metadata summary refreshing every 1 second. [2024-04-26 06:18:25,79] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. [2024-04-26 06:18:25,79] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. [2024-04-26 06:18:25,81] [warn] 'docker.hash-lookup.gcr-api-queries-per-100-seconds' is being deprecated, use 'docker.hash-lookup.gcr.throttle' instead (see reference.conf) [2024-04-26 06:18:25,81] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. [2024-04-26 06:18:25,88] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. [2024-04-26 06:18:25,92] [info] SingleWorkflowRunnerActor: Version 58 [2024-04-26 06:18:25,92] [info] SingleWorkflowRunnerActor: Submitting workflow [2024-04-26 06:18:25,95] [info] Unspecified type (Unspecified version) workflow 38537635-4551-45f3-bc4d-9d03c22a39c8 submitted [2024-04-26 06:18:25,97] [info] SingleWorkflowRunnerActor: Workflow submitted 38537635-4551-45f3-bc4d-9d03c22a39c8 [2024-04-26 06:18:25,97] [info] 1 new workflows fetched by cromid-3d67e9c: 38537635-4551-45f3-bc4d-9d03c22a39c8 [2024-04-26 06:18:25,98] [info] WorkflowManagerActor Starting workflow 38537635-4551-45f3-bc4d-9d03c22a39c8 [2024-04-26 06:18:25,99] [info] WorkflowManagerActor Successfully started WorkflowActor-38537635-4551-45f3-bc4d-9d03c22a39c8 [2024-04-26 06:18:25,99] [info] Retrieved 1 workflows from the WorkflowStoreActor [2024-04-26 06:18:26,01] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. [2024-04-26 06:18:26,08] [info] MaterializeWorkflowDescriptorActor [38537635]: Parsing workflow as WDL 1.0 [2024-04-26 06:18:27,50] [info] MaterializeWorkflowDescriptorActor [38537635]: Call-to-Backend assignments: annotate_variants_wf.annotate_splice_distance -> LocalExample, annotate_variants_wf.annotate_homopolymers_n_entropy -> LocalExample, annotate_variants_wf.annotate_RNA_editing -> LocalExample, annotate_variants_wf.annotate_blat_ED -> LocalExample, annotate_variants_wf.annotate_cosmic_variants -> LocalExample, annotate_variants_wf.open_cravat -> LocalExample, annotate_variants_wf.annotate_gnomad -> LocalExample, ctat_mutations.BaseRecalibrator -> LocalExample, ctat_mutations.SplitIntervals -> LocalExample, ctat_mutations.SplitReads -> LocalExample, ctat_mutations.ApplyBQSR -> LocalExample, ctat_mutations.CancerVariantReport -> LocalExample, ctat_mutations.HaplotypeCallerInterval -> LocalExample, ctat_mutations.StarAlign -> LocalExample, ctat_mutations.VariantFiltration -> LocalExample, annotate_variants_wf.annotate_repeats -> LocalExample, ctat_mutations.HaplotypeCallerExtra -> LocalExample, ctat_mutations.MergeVCFs -> LocalExample, annotate_variants_wf.rename_vcf -> LocalExample, annotate_variants_wf.annotate_dbsnp -> LocalExample, ctat_mutations.AddOrReplaceReadGroups -> LocalExample, ctat_mutations.CreateFastaIndex -> LocalExample, ctat_mutations.MergeRealignedBams -> LocalExample, ctat_mutations.SplitNCigarReads -> LocalExample, ctat_mutations.HaplotypeCaller -> LocalExample, ctat_mutations.MarkDuplicates -> LocalExample, annotate_variants_wf.annotate_PASS_reads -> LocalExample, annotate_variants_wf.left_norm_vcf -> LocalExample, ctat_mutations.MergeFastas -> LocalExample, ctat_mutations.mm2 -> LocalExample, ctat_mutations.FilterCancerVariants -> LocalExample, ctat_mutations.MergePrimaryAndExtraVCFs -> LocalExample, annotate_variants_wf.snpEff -> LocalExample [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [preemptible, bootDiskSizeGb, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [preemptible, bootDiskSizeGb, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [memory, disks, preemptible, docker] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,64] [warn] LocalExample [38537635]: Key/s [docker, memory, disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [docker, memory, disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, bootDiskSizeGb, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [disks, docker, memory, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [docker, memory, disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [disks, docker, memory, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, bootDiskSizeGb, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:27,65] [warn] LocalExample [38537635]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-26 06:18:30,89] [info] Not triggering log of token queue status. Effective log interval = None [2024-04-26 06:18:34,07] [info] WorkflowExecutionActor-38537635-4551-45f3-bc4d-9d03c22a39c8 [38537635]: Starting ctat_mutations.VariantFiltration [2024-04-26 06:18:34,90] [info] Assigned new job execution tokens to the following groups: 38537635: 1 [2024-04-26 06:18:35,06] [info] 38537635-4551-45f3-bc4d-9d03c22a39c8-EngineJobExecutionActor-ctat_mutations.VariantFiltration:NA:1 [38537635]: Could not copy a suitable cache hit for 38537635:ctat_mutations.VariantFiltration:-1:1. No copy attempts were made. [2024-04-26 06:18:35,08] [warn] BackgroundConfigAsyncJobExecutionActor [38537635ctat_mutations.VariantFiltration:NA:1]: Unrecognized runtime attribute keys: preemptible, disks, docker, cpu, memory [2024-04-26 06:18:35,11] [warn] Localization via hard link has failed: /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/817306935/ref_genome.fa.fai -> /ctat_genome_lib_dir/ref_genome.fa.fai: Invalid cross-device link [2024-04-26 06:18:35,12] [warn] Localization via hard link has failed: /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/817306935/ref_genome.fa -> /ctat_genome_lib_dir/ref_genome.fa: Invalid cross-device link [2024-04-26 06:18:35,12] [warn] Localization via hard link has failed: /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/817306935/ref_genome.dict -> /ctat_genome_lib_dir/ref_genome.dict: Invalid cross-device link [2024-04-26 06:18:35,15] [info] BackgroundConfigAsyncJobExecutionActor [38537635ctat_mutations.VariantFiltration:NA:1]: set -ex # monitor_script.sh & boosting_method="none" if [ "$boosting_method" == "none" ]; then gatk --java-options "-Xmx2500m" \ VariantFiltration \ --R /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/817306935/ref_genome.fa \ --V /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/-1064440064/mgp_REL2021_snps.vcf.gz \ --window 35 \ --cluster 3 \ --filter-name "FS" \ --filter "FS > 30.0" \ --filter-name "QD" \ --filter "QD < 2.0" \ --filter-name "SPLICEDIST" \ --filter "DJ < 3" \ -O tmp.vcf # note, no hard-filtering applied to indels currently gatk --java-options "-Xmx2500m" \ SelectVariants \ --R /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/817306935/ref_genome.fa \ --V tmp.vcf \ --exclude-filtered \ -O mm39.filtered.vcf.gz else ############## ## snps first: /usr/local/src/ctat-mutations/src/annotated_vcf_to_feature_matrix.py \ --vcf /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/-1064440064/mgp_REL2021_snps.vcf.gz \ --features AC,ALT,BaseQRankSum,DJ,DP,ED,Entropy,ExcessHet,FS,Homopolymer,LEN,MLEAF,MMF,QUAL,REF,RPT,RS,ReadPosRankSum,SAO,SOR,TCR,TDM,VAF,VMMF \ --snps \ --output none.snps.feature_matrix /usr/local/src/ctat-mutations/src/VariantBoosting/Apply_ML.py \ --feature_matrix none.snps.feature_matrix \ --snps \ --features AC,ALT,BaseQRankSum,DJ,DP,ED,Entropy,ExcessHet,FS,Homopolymer,LEN,MLEAF,MMF,QUAL,REF,RPT,RS,ReadPosRankSum,SAO,SOR,TCR,TDM,VAF,VMMF \ --predictor classifier \ --model none \ --output none.classifier.snps.feature_matrix.wPreds indel_boost_output="" if [ "false" == "true" ] ; then ############## ## indels next /usr/local/src/ctat-mutations/src/annotated_vcf_to_feature_matrix.py \ --vcf /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/-1064440064/mgp_REL2021_snps.vcf.gz \ --features AC,ALT,BaseQRankSum,DJ,DP,ED,Entropy,ExcessHet,FS,Homopolymer,LEN,MLEAF,MMF,QUAL,REF,RPT,RS,ReadPosRankSum,SAO,SOR,TCR,TDM,VAF,VMMF \ --indels \ --output none.indels.feature_matrix /usr/local/src/ctat-mutations/src/VariantBoosting/Apply_ML.py \ --feature_matrix none.indels.feature_matrix \ --indels \ --features AC,ALT,BaseQRankSum,DJ,DP,ED,Entropy,ExcessHet,FS,Homopolymer,LEN,MLEAF,MMF,QUAL,REF,RPT,RS,ReadPosRankSum,SAO,SOR,TCR,TDM,VAF,VMMF \ --predictor classifier \ --model none \ --output none.classifier.indels.feature_matrix.wPreds indel_boost_output="none.classifier.indels.feature_matrix.wPreds" fi ######### ## combine predictions into single output vcf /usr/local/src/ctat-mutations/src/annotate_boosted_vcf.py \ --vcf_in /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/-1064440064/mgp_REL2021_snps.vcf.gz \ --boosted_variants_matrix none.classifier.snps.feature_matrix.wPreds $indel_boost_output \ --boost_type classifier:none \ --vcf_out none.classifier.vcf bgzip -c none.classifier.vcf > mm39.filtered.vcf.gz fi [2024-04-26 06:18:35,19] [info] BackgroundConfigAsyncJobExecutionActor [38537635ctat_mutations.VariantFiltration:NA:1]: executing: /usr/bin/env bash /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/execution/script [2024-04-26 06:18:35,80] [info] BackgroundConfigAsyncJobExecutionActor [38537635ctat_mutations.VariantFiltration:NA:1]: job id: 202 [2024-04-26 06:18:35,81] [info] BackgroundConfigAsyncJobExecutionActor [38537635ctat_mutations.VariantFiltration:NA:1]: Status change from - to WaitingForReturnCode [2024-04-26 06:18:40,96] [info] BackgroundConfigAsyncJobExecutionActor [38537635ctat_mutations.VariantFiltration:NA:1]: Status change from WaitingForReturnCode to Done [2024-04-26 06:20:37,53] [info] WorkflowManagerActor Workflow 38537635-4551-45f3-bc4d-9d03c22a39c8 failed (during ExecutingWorkflowState): Job ctat_mutations.VariantFiltration:NA:1 exited with return code 3 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/execution/stderr. [First 3000 bytes]:+ boosting_method=none + '[' none == none ']' + gatk --java-options -Xmx2500m VariantFiltration --R /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/817306935/ref_genome.fa --V /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/-1064440064/mgp_REL2021_snps.vcf.gz --window 35 --cluster 3 --filter-name FS --filter 'FS > 30.0' --filter-name QD --filter 'QD < 2.0' --filter-name SPLICEDIST --filter 'DJ < 3' -O tmp.vcf Using GATK jar /usr/local/src/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx2500m -jar /usr/local/src/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar VariantFiltration --R /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/817306935/ref_genome.fa --V /home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/inputs/-1064440064/mgp_REL2021_snps.vcf.gz --window 35 --cluster 3 --filter-name FS --filter FS > 30.0 --filter-name QD --filter QD < 2.0 --filter-name SPLICEDIST --filter DJ < 3 -O tmp.vcf Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/home/lowlife/CTAT-mutations/bam/ctat_mutations_outdir/cromwell-executions/ctat_mutations/38537635-4551-45f3-bc4d-9d03c22a39c8/call-VariantFiltration/tmp.e4caa4cc 06:18:38.311 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/src/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Apr 26, 2024 6:18:38 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 06:18:38.598 INFO VariantFiltration - ------------------------------------------------------------ 06:18:38.599 INFO VariantFiltration - The Genome Analysis Toolkit (GATK) v4.1.9.0 06:18:38.599 INFO VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/ 06:18:38.599 INFO VariantFiltration - Executing as root@d5043192917d on Linux v5.15.146.1-microsoft-standard-WSL2 amd64 06:18:38.599 INFO VariantFiltration - Java runtime: OpenJDK 64-Bit Server VM v11.0.22+7-post-Ubuntu-0ubuntu220.04.1 06:18:38.599 INFO VariantFiltration - Start Date/Time: April 26, 2024 at 6:18:38 AM GMT 06:18:38.599 INFO VariantFiltration - ------------------------------------------------------------ 06:18:38.599 INFO VariantFiltration - ------------------------------------------------------------ 06:18:38.600 INFO VariantFiltration - HTSJDK Version: 2.23.0 06:18:38.600 INFO VariantFiltratio [2024-04-26 06:20:37,53] [info] WorkflowManagerActor WorkflowActor-38537635-4551-45f3-bc4d-9d03c22a39c8 is in a terminal state: WorkflowFailedState [2024-04-26 06:20:44,72] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'. [2024-04-26 06:20:45,91] [info] SingleWorkflowRunnerActor writing metadata to /tmp/tmpxh19swm2.json [2024-04-26 06:20:45,93] [info] Workflow polling stopped [2024-04-26 06:20:45,93] [info] 0 workflows released by cromid-3d67e9c [2024-04-26 06:20:45,94] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds [2024-04-26 06:20:45,94] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds [2024-04-26 06:20:45,94] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds [2024-04-26 06:20:45,94] [info] JobExecutionTokenDispenser stopped [2024-04-26 06:20:45,94] [info] Aborting all running workflows. [2024-04-26 06:20:45,94] [info] WorkflowStoreActor stopped [2024-04-26 06:20:45,94] [info] WorkflowLogCopyRouter stopped [2024-04-26 06:20:45,94] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds [2024-04-26 06:20:45,94] [info] WorkflowManagerActor All workflows finished [2024-04-26 06:20:45,94] [info] WorkflowManagerActor stopped [2024-04-26 06:20:46,11] [info] Connection pools shut down [2024-04-26 06:20:46,11] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds [2024-04-26 06:20:46,11] [info] Shutting down JobStoreActor - Timeout = 1800 seconds [2024-04-26 06:20:46,11] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds [2024-04-26 06:20:46,11] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds [2024-04-26 06:20:46,11] [info] SubWorkflowStoreActor stopped [2024-04-26 06:20:46,11] [info] Shutting down DockerHashActor - Timeout = 1800 seconds [2024-04-26 06:20:46,11] [info] Shutting down IoProxy - Timeout = 1800 seconds [2024-04-26 06:20:46,11] [info] CallCacheWriteActor Shutting down: 0 queued messages to process [2024-04-26 06:20:46,11] [info] JobStoreActor stopped [2024-04-26 06:20:46,11] [info] CallCacheWriteActor stopped [2024-04-26 06:20:46,11] [info] WriteMetadataActor Shutting down: 0 queued messages to process [2024-04-26 06:20:46,11] [info] KvWriteActor Shutting down: 0 queued messages to process [2024-04-26 06:20:46,11] [info] IoProxy stopped [2024-04-26 06:20:46,11] [info] ServiceRegistryActor stopped [2024-04-26 06:20:46,11] [info] DockerHashActor stopped [2024-04-26 06:20:46,13] [info] Database closed [2024-04-26 06:20:46,13] [info] Stream materializer shut down [2024-04-26 06:20:46,13] [info] WDL HTTP import resolver closed