[2024-04-19 06:04:22,36] [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 [2024-04-19 06:04:22,63] [info] dataFileCache open start [2024-04-19 06:04:22,65] [info] dataFileCache open end [2024-04-19 06:04:22,71] [info] checkpointClose start [2024-04-19 06:04:22,72] [info] checkpointClose synched [2024-04-19 06:04:22,73] [info] checkpointClose script done [2024-04-19 06:04:22,73] [info] dataFileCache commit start [2024-04-19 06:04:22,75] [info] dataFileCache commit end [2024-04-19 06:04:22,77] [info] checkpointClose end [2024-04-19 06:04:25,37] [info] Checkpoint start [2024-04-19 06:04:25,38] [info] checkpointClose start [2024-04-19 06:04:25,39] [info] checkpointClose synched [2024-04-19 06:04:25,41] [info] checkpointClose script done [2024-04-19 06:04:25,41] [info] dataFileCache commit start [2024-04-19 06:04:25,41] [info] dataFileCache commit end [2024-04-19 06:04:25,42] [info] checkpointClose end [2024-04-19 06:04:25,43] [info] Checkpoint end - txts: 9733 [2024-04-19 06:04:25,47] [info] Checkpoint start [2024-04-19 06:04:25,47] [info] checkpointClose start [2024-04-19 06:04:25,48] [info] checkpointClose synched [2024-04-19 06:04:25,49] [info] checkpointClose script done [2024-04-19 06:04:25,49] [info] dataFileCache commit start [2024-04-19 06:04:25,49] [info] dataFileCache commit end [2024-04-19 06:04:25,50] [info] checkpointClose end [2024-04-19 06:04:25,50] [info] Checkpoint end - txts: 9749 [2024-04-19 06:04:25,51] [info] Checkpoint start [2024-04-19 06:04:25,51] [info] checkpointClose start [2024-04-19 06:04:25,51] [info] checkpointClose synched [2024-04-19 06:04:25,52] [info] checkpointClose script done [2024-04-19 06:04:25,52] [info] dataFileCache commit start [2024-04-19 06:04:25,52] [info] dataFileCache commit end [2024-04-19 06:04:25,53] [info] checkpointClose end [2024-04-19 06:04:25,53] [info] Checkpoint end - txts: 9751 [2024-04-19 06:04:26,88] [info] Checkpoint start [2024-04-19 06:04:26,88] [info] checkpointClose start [2024-04-19 06:04:26,90] [info] checkpointClose synched [2024-04-19 06:04:26,90] [info] checkpointClose script done [2024-04-19 06:04:26,90] [info] dataFileCache commit start [2024-04-19 06:04:26,91] [info] dataFileCache commit end [2024-04-19 06:04:26,92] [info] checkpointClose end [2024-04-19 06:04:26,92] [info] Checkpoint end - txts: 9774 [2024-04-19 06:04:26,92] [info] Checkpoint start [2024-04-19 06:04:26,92] [info] checkpointClose start [2024-04-19 06:04:26,93] [info] checkpointClose synched [2024-04-19 06:04:26,93] [info] checkpointClose script done [2024-04-19 06:04:26,94] [info] dataFileCache commit start [2024-04-19 06:04:26,94] [info] dataFileCache commit end [2024-04-19 06:04:26,95] [info] checkpointClose end [2024-04-19 06:04:26,95] [info] Checkpoint end - txts: 9776 [2024-04-19 06:04:27,04] [info] Checkpoint start [2024-04-19 06:04:27,04] [info] checkpointClose start [2024-04-19 06:04:27,04] [info] checkpointClose synched [2024-04-19 06:04:27,05] [info] checkpointClose script done [2024-04-19 06:04:27,05] [info] dataFileCache commit start [2024-04-19 06:04:27,06] [info] dataFileCache commit end [2024-04-19 06:04:27,07] [info] checkpointClose end [2024-04-19 06:04:27,07] [info] Checkpoint end - txts: 9778 [2024-04-19 06:04:27,07] [info] Checkpoint start [2024-04-19 06:04:27,07] [info] checkpointClose start [2024-04-19 06:04:27,08] [info] checkpointClose synched [2024-04-19 06:04:27,08] [info] checkpointClose script done [2024-04-19 06:04:27,08] [info] dataFileCache commit start [2024-04-19 06:04:27,09] [info] dataFileCache commit end [2024-04-19 06:04:27,11] [info] checkpointClose end [2024-04-19 06:04:27,11] [info] Checkpoint end - txts: 9785 [2024-04-19 06:04:27,11] [info] Checkpoint start [2024-04-19 06:04:27,11] [info] checkpointClose start [2024-04-19 06:04:27,11] [info] checkpointClose synched [2024-04-19 06:04:27,12] [info] checkpointClose script done [2024-04-19 06:04:27,12] [info] dataFileCache commit start [2024-04-19 06:04:27,12] [info] dataFileCache commit end [2024-04-19 06:04:27,13] [info] checkpointClose end [2024-04-19 06:04:27,14] [info] Checkpoint end - txts: 9787 [2024-04-19 06:04:27,14] [info] Checkpoint start [2024-04-19 06:04:27,14] [info] checkpointClose start [2024-04-19 06:04:27,14] [info] checkpointClose synched [2024-04-19 06:04:27,15] [info] checkpointClose script done [2024-04-19 06:04:27,15] [info] dataFileCache commit start [2024-04-19 06:04:27,15] [info] dataFileCache commit end [2024-04-19 06:04:27,16] [info] checkpointClose end [2024-04-19 06:04:27,16] [info] Checkpoint end - txts: 9789 [2024-04-19 06:04:27,17] [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 [2024-04-19 06:04:27,18] [info] Checkpoint start [2024-04-19 06:04:27,18] [info] checkpointClose start [2024-04-19 06:04:27,19] [info] checkpointClose synched [2024-04-19 06:04:27,19] [info] checkpointClose script done [2024-04-19 06:04:27,19] [info] dataFileCache commit start [2024-04-19 06:04:27,20] [info] dataFileCache commit end [2024-04-19 06:04:27,21] [info] checkpointClose end [2024-04-19 06:04:27,21] [info] Checkpoint end - txts: 9797 [2024-04-19 06:04:27,22] [info] Checkpoint start [2024-04-19 06:04:27,22] [info] checkpointClose start [2024-04-19 06:04:27,23] [info] checkpointClose synched [2024-04-19 06:04:27,23] [info] checkpointClose script done [2024-04-19 06:04:27,23] [info] dataFileCache commit start [2024-04-19 06:04:27,24] [info] dataFileCache commit end [2024-04-19 06:04:27,25] [info] checkpointClose end [2024-04-19 06:04:27,25] [info] Checkpoint end - txts: 9813 [2024-04-19 06:04:27,25] [info] Checkpoint start [2024-04-19 06:04:27,25] [info] checkpointClose start [2024-04-19 06:04:27,26] [info] checkpointClose synched [2024-04-19 06:04:27,26] [info] checkpointClose script done [2024-04-19 06:04:27,26] [info] dataFileCache commit start [2024-04-19 06:04:27,27] [info] dataFileCache commit end [2024-04-19 06:04:27,28] [info] checkpointClose end [2024-04-19 06:04:27,28] [info] Checkpoint end - txts: 9815 [2024-04-19 06:04:27,36] [info] Checkpoint start [2024-04-19 06:04:27,36] [info] checkpointClose start [2024-04-19 06:04:27,36] [info] checkpointClose synched [2024-04-19 06:04:27,37] [info] checkpointClose script done [2024-04-19 06:04:27,37] [info] dataFileCache commit start [2024-04-19 06:04:27,37] [info] dataFileCache commit end [2024-04-19 06:04:27,38] [info] checkpointClose end [2024-04-19 06:04:27,38] [info] Checkpoint end - txts: 9838 [2024-04-19 06:04:27,39] [info] Checkpoint start [2024-04-19 06:04:27,39] [info] checkpointClose start [2024-04-19 06:04:27,39] [info] checkpointClose synched [2024-04-19 06:04:27,40] [info] checkpointClose script done [2024-04-19 06:04:27,40] [info] dataFileCache commit start [2024-04-19 06:04:27,40] [info] dataFileCache commit end [2024-04-19 06:04:27,41] [info] checkpointClose end [2024-04-19 06:04:27,41] [info] Checkpoint end - txts: 9840 [2024-04-19 06:04:27,42] [info] Checkpoint start [2024-04-19 06:04:27,42] [info] checkpointClose start [2024-04-19 06:04:27,42] [info] checkpointClose synched [2024-04-19 06:04:27,43] [info] checkpointClose script done [2024-04-19 06:04:27,43] [info] dataFileCache commit start [2024-04-19 06:04:27,43] [info] dataFileCache commit end [2024-04-19 06:04:27,44] [info] checkpointClose end [2024-04-19 06:04:27,44] [info] Checkpoint end - txts: 9842 [2024-04-19 06:04:27,45] [info] Checkpoint start [2024-04-19 06:04:27,45] [info] checkpointClose start [2024-04-19 06:04:27,45] [info] checkpointClose synched [2024-04-19 06:04:27,46] [info] checkpointClose script done [2024-04-19 06:04:27,46] [info] dataFileCache commit start [2024-04-19 06:04:27,47] [info] dataFileCache commit end [2024-04-19 06:04:27,48] [info] checkpointClose end [2024-04-19 06:04:27,48] [info] Checkpoint end - txts: 9849 [2024-04-19 06:04:27,48] [info] Checkpoint start [2024-04-19 06:04:27,48] [info] checkpointClose start [2024-04-19 06:04:27,48] [info] checkpointClose synched [2024-04-19 06:04:27,49] [info] checkpointClose script done [2024-04-19 06:04:27,49] [info] dataFileCache commit start [2024-04-19 06:04:27,49] [info] dataFileCache commit end [2024-04-19 06:04:27,50] [info] checkpointClose end [2024-04-19 06:04:27,51] [info] Checkpoint end - txts: 9851 [2024-04-19 06:04:27,51] [info] Checkpoint start [2024-04-19 06:04:27,51] [info] checkpointClose start [2024-04-19 06:04:27,51] [info] checkpointClose synched [2024-04-19 06:04:27,52] [info] checkpointClose script done [2024-04-19 06:04:27,52] [info] dataFileCache commit start [2024-04-19 06:04:27,52] [info] dataFileCache commit end [2024-04-19 06:04:27,53] [info] checkpointClose end [2024-04-19 06:04:27,53] [info] Checkpoint end - txts: 9853 [2024-04-19 06:04:27,68] [info] Slf4jLogger started [2024-04-19 06:04:27,80] [info] Workflow heartbeat configuration: { "cromwellId" : "cromid-1d55cbb", "heartbeatInterval" : "2 minutes", "ttl" : "10 minutes", "failureShutdownDuration" : "5 minutes", "writeBatchSize" : 10000, "writeThreshold" : 10000 } [2024-04-19 06:04:27,83] [info] Metadata summary refreshing every 1 second. [2024-04-19 06:04:27,84] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. [2024-04-19 06:04:27,84] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. [2024-04-19 06:04:27,86] [warn] 'docker.hash-lookup.gcr-api-queries-per-100-seconds' is being deprecated, use 'docker.hash-lookup.gcr.throttle' instead (see reference.conf) [2024-04-19 06:04:27,86] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. [2024-04-19 06:04:27,94] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. [2024-04-19 06:04:28,00] [info] SingleWorkflowRunnerActor: Version 58 [2024-04-19 06:04:28,01] [info] SingleWorkflowRunnerActor: Submitting workflow [2024-04-19 06:04:28,04] [info] Unspecified type (Unspecified version) workflow 599bcffc-9df3-46d6-ab4b-6e04d7006fed submitted [2024-04-19 06:04:28,06] [info] SingleWorkflowRunnerActor: Workflow submitted 599bcffc-9df3-46d6-ab4b-6e04d7006fed [2024-04-19 06:04:28,06] [info] 1 new workflows fetched by cromid-1d55cbb: 599bcffc-9df3-46d6-ab4b-6e04d7006fed [2024-04-19 06:04:28,07] [info] WorkflowManagerActor Starting workflow 599bcffc-9df3-46d6-ab4b-6e04d7006fed [2024-04-19 06:04:28,08] [info] WorkflowManagerActor Successfully started WorkflowActor-599bcffc-9df3-46d6-ab4b-6e04d7006fed [2024-04-19 06:04:28,08] [info] Retrieved 1 workflows from the WorkflowStoreActor [2024-04-19 06:04:28,10] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. [2024-04-19 06:04:28,17] [info] MaterializeWorkflowDescriptorActor [599bcffc]: Parsing workflow as WDL 1.0 [2024-04-19 06:04:29,49] [info] MaterializeWorkflowDescriptorActor [599bcffc]: Call-to-Backend assignments: ctat_mutations.MergePrimaryAndExtraVCFs -> LocalExample, ctat_mutations.HaplotypeCallerExtra -> LocalExample, ctat_mutations.MergeRealignedBams -> LocalExample, ctat_mutations.HaplotypeCallerInterval -> LocalExample, ctat_mutations.CreateFastaIndex -> LocalExample, ctat_mutations.MarkDuplicates -> LocalExample, annotate_variants_wf.rename_vcf -> LocalExample, annotate_variants_wf.annotate_blat_ED -> LocalExample, ctat_mutations.ApplyBQSR -> LocalExample, annotate_variants_wf.annotate_dbsnp -> LocalExample, annotate_variants_wf.annotate_gnomad -> LocalExample, ctat_mutations.VariantFiltration -> LocalExample, annotate_variants_wf.annotate_homopolymers_n_entropy -> LocalExample, ctat_mutations.FilterCancerVariants -> LocalExample, annotate_variants_wf.annotate_repeats -> LocalExample, ctat_mutations.StarAlign -> LocalExample, annotate_variants_wf.annotate_PASS_reads -> LocalExample, ctat_mutations.HaplotypeCaller -> LocalExample, ctat_mutations.SplitIntervals -> LocalExample, ctat_mutations.MergeFastas -> LocalExample, annotate_variants_wf.open_cravat -> LocalExample, annotate_variants_wf.annotate_cosmic_variants -> LocalExample, ctat_mutations.CancerVariantReport -> LocalExample, annotate_variants_wf.snpEff -> LocalExample, annotate_variants_wf.left_norm_vcf -> LocalExample, annotate_variants_wf.annotate_RNA_editing -> LocalExample, ctat_mutations.MergeVCFs -> LocalExample, ctat_mutations.mm2 -> LocalExample, ctat_mutations.SplitReads -> LocalExample, ctat_mutations.BaseRecalibrator -> LocalExample, ctat_mutations.SplitNCigarReads -> LocalExample, annotate_variants_wf.annotate_splice_distance -> LocalExample, ctat_mutations.AddOrReplaceReadGroups -> LocalExample [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [docker, memory, disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [docker, memory, disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, bootDiskSizeGb, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [disks, docker, memory, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [memory, disks, preemptible, docker] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,58] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [docker, memory, disks, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, bootDiskSizeGb, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, bootDiskSizeGb, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, bootDiskSizeGb, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [disks, docker, memory, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [preemptible, disks, docker, cpu, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:29,59] [warn] LocalExample [599bcffc]: Key/s [memory, disks, docker, preemptible] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2024-04-19 06:04:32,95] [info] Not triggering log of token queue status. Effective log interval = None [2024-04-19 06:04:36,87] [info] WorkflowExecutionActor-599bcffc-9df3-46d6-ab4b-6e04d7006fed [599bcffc]: Starting ctat_mutations.StarAlign, ctat_mutations.SplitIntervals [2024-04-19 06:04:36,96] [info] Assigned new job execution tokens to the following groups: 599bcffc: 2 [2024-04-19 06:04:37,06] [info] 599bcffc-9df3-46d6-ab4b-6e04d7006fed-EngineJobExecutionActor-ctat_mutations.SplitIntervals:NA:1 [599bcffc]: Could not copy a suitable cache hit for 599bcffc:ctat_mutations.SplitIntervals:-1:1. No copy attempts were made. [2024-04-19 06:04:37,08] [warn] BackgroundConfigAsyncJobExecutionActor [599bcffcctat_mutations.SplitIntervals:NA:1]: Unrecognized runtime attribute keys: preemptible, bootDiskSizeGb, disks, docker, cpu, memory [2024-04-19 06:04:37,10] [warn] Localization via hard link has failed: /home/lowlife/CTAT-mutations/fastqc_trimmed_results_39/ctat_mutations_outdir/cromwell-executions/ctat_mutations/599bcffc-9df3-46d6-ab4b-6e04d7006fed/call-SplitIntervals/inputs/817306935/ref_genome.dict -> /ctat_genome_lib_dir/ref_genome.dict: Invalid cross-device link [2024-04-19 06:04:37,10] [warn] Localization via hard link has failed: /home/lowlife/CTAT-mutations/fastqc_trimmed_results_39/ctat_mutations_outdir/cromwell-executions/ctat_mutations/599bcffc-9df3-46d6-ab4b-6e04d7006fed/call-SplitIntervals/inputs/817306935/ref_genome.fa -> /ctat_genome_lib_dir/ref_genome.fa: Invalid cross-device link [2024-04-19 06:04:37,10] [warn] Localization via hard link has failed: /home/lowlife/CTAT-mutations/fastqc_trimmed_results_39/ctat_mutations_outdir/cromwell-executions/ctat_mutations/599bcffc-9df3-46d6-ab4b-6e04d7006fed/call-SplitIntervals/inputs/817306935/ref_genome.fa.fai -> /ctat_genome_lib_dir/ref_genome.fa.fai: Invalid cross-device link [2024-04-19 06:04:37,12] [info] BackgroundConfigAsyncJobExecutionActor [599bcffcctat_mutations.SplitIntervals:NA:1]: set -e # monitor_script.sh & mkdir interval-files gatk --java-options "-Xmx1500m" \ SplitIntervals \ -R /home/lowlife/CTAT-mutations/fastqc_trimmed_results_39/ctat_mutations_outdir/cromwell-executions/ctat_mutations/599bcffc-9df3-46d6-ab4b-6e04d7006fed/call-SplitIntervals/inputs/817306935/ref_genome.fa \ -scatter 6 \ -O interval-files \ cp interval-files/*.interval_list . [2024-04-19 06:04:37,16] [info] BackgroundConfigAsyncJobExecutionActor [599bcffcctat_mutations.SplitIntervals:NA:1]: executing: /usr/bin/env bash /home/lowlife/CTAT-mutations/fastqc_trimmed_results_39/ctat_mutations_outdir/cromwell-executions/ctat_mutations/599bcffc-9df3-46d6-ab4b-6e04d7006fed/call-SplitIntervals/execution/script [2024-04-19 06:04:37,87] [info] BackgroundConfigAsyncJobExecutionActor [599bcffcctat_mutations.SplitIntervals:NA:1]: job id: 216 [2024-04-19 06:04:37,87] [info] BackgroundConfigAsyncJobExecutionActor [599bcffcctat_mutations.SplitIntervals:NA:1]: Status change from - to WaitingForReturnCode [2024-04-19 06:04:39,42] [info] BackgroundConfigAsyncJobExecutionActor [599bcffcctat_mutations.SplitIntervals:NA:1]: Status change from WaitingForReturnCode to Done [2024-04-19 06:04:44,04] [info] WorkflowManagerActor Workflow 599bcffc-9df3-46d6-ab4b-6e04d7006fed failed (during ExecutingWorkflowState): cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for StarAlign: [Attempted 1 time(s)] - NoSuchFileException: /home/lowlife/CTAT-mutations/fastqc_trimmed_results_39/SRR10075970_read_1.fastq.gz Job ctat_mutations.SplitIntervals:NA:1 exited with return code 1 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/fastqc_trimmed_results_39/ctat_mutations_outdir/cromwell-executions/ctat_mutations/599bcffc-9df3-46d6-ab4b-6e04d7006fed/call-SplitIntervals/execution/stderr. [First 3000 bytes]: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 -Xmx1500m -jar /usr/local/src/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar SplitIntervals -R /home/lowlife/CTAT-mutations/fastqc_trimmed_results_39/ctat_mutations_outdir/cromwell-executions/ctat_mutations/599bcffc-9df3-46d6-ab4b-6e04d7006fed/call-SplitIntervals/inputs/817306935/ref_genome.fa -scatter 6 -O interval-files Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/home/lowlife/CTAT-mutations/fastqc_trimmed_results_39/ctat_mutations_outdir/cromwell-executions/ctat_mutations/599bcffc-9df3-46d6-ab4b-6e04d7006fed/call-SplitIntervals/tmp.71571d5a 06:04:38.432 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 19, 2024 6:04:38 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 06:04:38.540 INFO SplitIntervals - ------------------------------------------------------------ 06:04:38.540 INFO SplitIntervals - The Genome Analysis Toolkit (GATK) v4.1.9.0 06:04:38.540 INFO SplitIntervals - For support and documentation go to https://software.broadinstitute.org/gatk/ 06:04:38.540 INFO SplitIntervals - Executing as root@72afd449d708 on Linux v5.15.146.1-microsoft-standard-WSL2 amd64 06:04:38.540 INFO SplitIntervals - Java runtime: OpenJDK 64-Bit Server VM v11.0.20.1+1-post-Ubuntu-0ubuntu120.04 06:04:38.540 INFO SplitIntervals - Start Date/Time: April 19, 2024 at 6:04:38 AM GMT 06:04:38.540 INFO SplitIntervals - ------------------------------------------------------------ 06:04:38.541 INFO SplitIntervals - ------------------------------------------------------------ 06:04:38.541 INFO SplitIntervals - HTSJDK Version: 2.23.0 06:04:38.541 INFO SplitIntervals - Picard Version: 2.23.3 06:04:38.541 INFO SplitIntervals - HTSJDK Defaults.COMPRESSION_LEVEL : 2 06:04:38.541 INFO SplitIntervals - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 06:04:38.541 INFO SplitIntervals - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 06:04:38.541 INFO SplitIntervals - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 06:04:38.542 INFO SplitIntervals - Deflater: IntelDeflater 06:04:38.542 INFO SplitIntervals - Inflater: IntelInflater 06:04:38.542 INFO SplitIntervals - GCS max retries/reopens: 20 06:04:38.542 INFO SplitIntervals - Requester pays: disabled 06:04:38.542 INFO SplitIntervals - Initializing engine 06:04:38.615 INFO SplitIntervals - Done initializing engine 06:04:38.618 INFO SplitIntervals - Shutting down engine [April 19, 2024 at 6:04:38 AM GMT] org.broadinstitute.hellbender.tools.walkers.SplitIntervals done. Elapsed time: 0.00 minutes. Runtime.totalMemory() [2024-04-19 06:04:44,04] [info] WorkflowManagerActor WorkflowActor-599bcffc-9df3-46d6-ab4b-6e04d7006fed is in a terminal state: WorkflowFailedState [2024-04-19 06:04:48,17] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'. [2024-04-19 06:04:52,93] [info] SingleWorkflowRunnerActor writing metadata to /tmp/tmpznx4zh3q.json [2024-04-19 06:04:52,94] [info] Workflow polling stopped [2024-04-19 06:04:52,95] [info] 0 workflows released by cromid-1d55cbb [2024-04-19 06:04:52,95] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds [2024-04-19 06:04:52,96] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds [2024-04-19 06:04:52,96] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds [2024-04-19 06:04:52,96] [info] Aborting all running workflows. [2024-04-19 06:04:52,96] [info] JobExecutionTokenDispenser stopped [2024-04-19 06:04:52,96] [info] WorkflowStoreActor stopped [2024-04-19 06:04:52,96] [info] WorkflowLogCopyRouter stopped [2024-04-19 06:04:52,96] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds [2024-04-19 06:04:52,96] [info] WorkflowManagerActor All workflows finished [2024-04-19 06:04:52,96] [info] WorkflowManagerActor stopped [2024-04-19 06:04:53,10] [info] Connection pools shut down [2024-04-19 06:04:53,10] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds [2024-04-19 06:04:53,10] [info] Shutting down JobStoreActor - Timeout = 1800 seconds [2024-04-19 06:04:53,10] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds [2024-04-19 06:04:53,10] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds [2024-04-19 06:04:53,10] [info] SubWorkflowStoreActor stopped [2024-04-19 06:04:53,10] [info] Shutting down DockerHashActor - Timeout = 1800 seconds [2024-04-19 06:04:53,10] [info] CallCacheWriteActor Shutting down: 0 queued messages to process [2024-04-19 06:04:53,10] [info] Shutting down IoProxy - Timeout = 1800 seconds [2024-04-19 06:04:53,10] [info] CallCacheWriteActor stopped [2024-04-19 06:04:53,10] [info] JobStoreActor stopped [2024-04-19 06:04:53,10] [info] IoProxy stopped [2024-04-19 06:04:53,10] [info] KvWriteActor Shutting down: 0 queued messages to process [2024-04-19 06:04:53,10] [info] WriteMetadataActor Shutting down: 0 queued messages to process [2024-04-19 06:04:53,10] [info] ServiceRegistryActor stopped [2024-04-19 06:04:53,11] [info] DockerHashActor stopped [2024-04-19 06:04:53,12] [info] Database closed [2024-04-19 06:04:53,12] [info] Stream materializer shut down [2024-04-19 06:04:53,13] [info] WDL HTTP import resolver closed