/netapp/home/kirsty.jamieson/.bash_profile: line 7: syntax error: unexpected end of file [2018-12-05 09:29:31,09] [info] Running with database db.url = jdbc:hsqldb:mem:d8820c53-c532-47b1-b06f-08a471b1a602;shutdown=false;hsqldb.tx=mvcc [2018-12-05 09:30:15,67] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000 [2018-12-05 09:30:16,13] [info] [RenameWorkflowOptionsInMetadata] 100% [2018-12-05 09:30:16,22] [info] Running with database db.url = jdbc:hsqldb:mem:cf02f414-e244-493c-89be-e84cb061cc9f;shutdown=false;hsqldb.tx=mvcc [2018-12-05 09:30:16,59] [warn] This actor factory is deprecated. Please use cromwell.backend.google.pipelines.v1alpha2.PipelinesApiLifecycleActorFactory for PAPI v1 or cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory for PAPI v2 [2018-12-05 09:30:16,62] [warn] Couldn't find a suitable DSN, defaulting to a Noop one. [2018-12-05 09:30:16,62] [info] Using noop to send events. [2018-12-05 09:30:16,90] [info] Slf4jLogger started [2018-12-05 09:30:19,17] [info] Workflow heartbeat configuration: { "cromwellId" : "cromid-69dc7f6", "heartbeatInterval" : "2 minutes", "ttl" : "10 minutes", "writeBatchSize" : 10000, "writeThreshold" : 10000 } [2018-12-05 09:30:19,22] [info] Metadata summary refreshing every 2 seconds. [2018-12-05 09:30:19,32] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. [2018-12-05 09:30:19,33] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. [2018-12-05 09:30:19,33] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. [2018-12-05 09:30:19,93] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. [2018-12-05 09:30:19,95] [info] JES batch polling interval is 33333 milliseconds [2018-12-05 09:30:19,95] [info] JES batch polling interval is 33333 milliseconds [2018-12-05 09:30:19,96] [info] JES batch polling interval is 33333 milliseconds [2018-12-05 09:30:19,96] [info] SingleWorkflowRunnerActor: Version 34 [2018-12-05 09:30:19,96] [info] PAPIQueryManager Running with 3 workers [2018-12-05 09:30:19,96] [info] SingleWorkflowRunnerActor: Submitting workflow [2018-12-05 09:30:20,00] [info] Unspecified type (Unspecified version) workflow 6155fd91-835b-4644-b8d5-c4a8642a3263 submitted [2018-12-05 09:30:20,05] [info] SingleWorkflowRunnerActor: Workflow submitted 6155fd91-835b-4644-b8d5-c4a8642a3263 [2018-12-05 09:30:20,05] [info] 1 new workflows fetched [2018-12-05 09:30:20,06] [info] WorkflowManagerActor Starting workflow 6155fd91-835b-4644-b8d5-c4a8642a3263 [2018-12-05 09:30:20,06] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData [2018-12-05 09:30:20,06] [info] WorkflowManagerActor Successfully started WorkflowActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [2018-12-05 09:30:20,06] [info] Retrieved 1 workflows from the WorkflowStoreActor [2018-12-05 09:30:20,07] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. [2018-12-05 09:30:20,67] [info] MaterializeWorkflowDescriptorActor [6155fd91]: Parsing workflow as WDL draft-2 [2018-12-05 09:30:45,08] [info] MaterializeWorkflowDescriptorActor [6155fd91]: Call-to-Backend assignments: atac.idr_pr -> Local, atac.trim_adapter -> Local, atac.pool_ta_pr1 -> Local, atac.macs2 -> Local, atac.pool_ta_pr2 -> Local, atac.macs2_pr1 -> Local, atac.reproducibility_overlap -> Local, atac.overlap_pr -> Local, atac.read_genome_tsv -> Local, atac.idr -> Local, atac.macs2_pooled -> Local, atac.ataqc -> Local, atac.bam2ta -> Local, atac.xcor -> Local, atac.spr -> Local, atac.overlap_ppr -> Local, atac.overlap -> Local, atac.macs2_ppr1 -> Local, atac.idr_ppr -> Local, atac.bowtie2 -> Local, atac.pool_ta -> Local, atac.macs2_ppr2 -> Local, atac.macs2_pr2 -> Local, atac.filter -> Local, atac.reproducibility_idr -> Local, atac.qc_report -> Local [2018-12-05 09:30:45,84] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,85] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,85] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,85] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,85] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,85] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,85] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,85] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,85] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,85] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,86] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,86] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,86] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,86] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,86] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,86] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,86] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,86] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,86] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,86] [warn] Local [6155fd91]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,87] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,87] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,87] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,87] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,87] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:45,87] [warn] Local [6155fd91]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-12-05 09:30:48,18] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Starting atac.read_genome_tsv [2018-12-05 09:30:48,18] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Condition met: 'enable_idr'. Running conditional section [2018-12-05 09:30:48,19] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Condition NOT met: 'enable_xcor'. Bypassing conditional section [2018-12-05 09:30:48,19] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Condition met: '!align_only && !true_rep_only && enable_idr'. Running conditional section [2018-12-05 09:30:48,19] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Condition met: 'enable_idr'. Running conditional section [2018-12-05 09:30:48,19] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Condition met: '!align_only && !true_rep_only'. Running conditional section [2018-12-05 09:30:48,20] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Condition met: '!true_rep_only'. Running conditional section [2018-12-05 09:30:49,06] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.read_genome_tsv:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:30:49,84] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.read_genome_tsv:NA:1]: cat /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-read_genome_tsv/inputs/-398504913/hg38.tsv [2018-12-05 09:30:51,40] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.read_genome_tsv:NA:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-read_genome_tsv/execution/script [2018-12-05 09:30:54,36] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.read_genome_tsv:NA:1]: job id: 26265 [2018-12-05 09:30:55,09] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.read_genome_tsv:NA:1]: Status change from - to WaitingForReturnCodeFile [2018-12-05 09:30:56,97] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.read_genome_tsv:NA:1]: Status change from WaitingForReturnCodeFile to Done [2018-12-05 09:31:00,47] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Starting atac.bam2ta (3 shards) [2018-12-05 09:31:00,95] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:31:00,95] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:2:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:31:00,96] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:31:01,22] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:2:1]: python $(which encode_bam2ta.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-bam2ta/shard-2/inputs/-1239304994/KJ066_R1_TRIM.trim.nodup.bam \ --paired-end \ \ --regex-grep-v-ta 'chrM' \ --subsample 0 \ --nth 2 [2018-12-05 09:31:01,25] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:1:1]: python $(which encode_bam2ta.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-bam2ta/shard-1/inputs/-1239304995/KJ065_R1_TRIM.trim.nodup.bam \ --paired-end \ \ --regex-grep-v-ta 'chrM' \ --subsample 0 \ --nth 2 [2018-12-05 09:31:01,27] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:0:1]: python $(which encode_bam2ta.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-bam2ta/shard-0/inputs/-1239304996/KJ064_R1_TRIM.trim.nodup.bam \ --paired-end \ \ --regex-grep-v-ta 'chrM' \ --subsample 0 \ --nth 2 [2018-12-05 09:31:01,29] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:2:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-bam2ta/shard-2/execution/script [2018-12-05 09:31:01,30] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:1:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-bam2ta/shard-1/execution/script [2018-12-05 09:31:01,32] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:0:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-bam2ta/shard-0/execution/script [2018-12-05 09:31:04,35] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:2:1]: job id: 26310 [2018-12-05 09:31:04,35] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:0:1]: job id: 26308 [2018-12-05 09:31:04,35] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:1:1]: job id: 26309 [2018-12-05 09:31:05,38] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:2:1]: Status change from - to WaitingForReturnCodeFile [2018-12-05 09:31:05,38] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:1:1]: Status change from - to WaitingForReturnCodeFile [2018-12-05 09:31:05,38] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:0:1]: Status change from - to WaitingForReturnCodeFile [2018-12-05 09:48:59,70] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:2:1]: Status change from WaitingForReturnCodeFile to Done [2018-12-05 09:56:44,08] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:1:1]: Status change from WaitingForReturnCodeFile to Done [2018-12-05 09:58:09,66] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.bam2ta:0:1]: Status change from WaitingForReturnCodeFile to Done [2018-12-05 09:58:13,67] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Condition met: 'length(tas_) > 1'. Running conditional section [2018-12-05 09:58:13,67] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Condition met: '!true_rep_only && length(tas_) > 1'. Running conditional section [2018-12-05 09:58:15,78] [info] WorkflowExecutionActor-6155fd91-835b-4644-b8d5-c4a8642a3263 [6155fd91]: Starting atac.pool_ta, atac.macs2 (3 shards), atac.spr (3 shards) [2018-12-05 09:58:15,95] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:58:15,95] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:58:15,95] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:2:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:58:15,95] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:58:15,95] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:58:15,95] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.pool_ta:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:58:15,95] [warn] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:2:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-12-05 09:58:15,97] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:0:1]: python $(which encode_spr.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-spr/shard-0/inputs/-1727468091/KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --paired-end [2018-12-05 09:58:15,99] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:2:1]: python $(which encode_spr.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-spr/shard-2/inputs/-1742986809/KJ066_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --paired-end [2018-12-05 09:58:15,99] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:2:1]: python $(which encode_macs2_atac.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-2/inputs/-1742986809/KJ066_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --gensz hs \ --chrsz /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-2/inputs/-398504913/hg38.chrom.sizes \ --cap-num-peak 300000 \ --pval-thresh 0.01 \ --smooth-win 150 \ --make-signal \ \ --blacklist /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-2/inputs/-398504913/hg38.blacklist.bed.gz # ugly part to deal with optional outputs with Google JES backend touch null [2018-12-05 09:58:15,99] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.pool_ta:NA:1]: python $(which encode_pool_ta.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-pool_ta/inputs/-1727468091/KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-pool_ta/inputs/-1735227450/KJ065_R1_TRIM.trim.nodup.tn5.tagAlign.gz /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-pool_ta/inputs/-1742986809/KJ066_R1_TRIM.trim.nodup.tn5.tagAlign.gz [2018-12-05 09:58:16,00] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:1:1]: python $(which encode_spr.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-spr/shard-1/inputs/-1735227450/KJ065_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --paired-end [2018-12-05 09:58:16,00] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:0:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-spr/shard-0/execution/script [2018-12-05 09:58:16,01] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:0:1]: python $(which encode_macs2_atac.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-0/inputs/-1727468091/KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --gensz hs \ --chrsz /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-0/inputs/-398504913/hg38.chrom.sizes \ --cap-num-peak 300000 \ --pval-thresh 0.01 \ --smooth-win 150 \ --make-signal \ \ --blacklist /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-0/inputs/-398504913/hg38.blacklist.bed.gz # ugly part to deal with optional outputs with Google JES backend touch null [2018-12-05 09:58:16,01] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:2:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-spr/shard-2/execution/script [2018-12-05 09:58:16,01] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:1:1]: python $(which encode_macs2_atac.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-1/inputs/-1735227450/KJ065_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --gensz hs \ --chrsz /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-1/inputs/-398504913/hg38.chrom.sizes \ --cap-num-peak 300000 \ --pval-thresh 0.01 \ --smooth-win 150 \ --make-signal \ \ --blacklist /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-1/inputs/-398504913/hg38.blacklist.bed.gz # ugly part to deal with optional outputs with Google JES backend touch null [2018-12-05 09:58:16,02] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.pool_ta:NA:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-pool_ta/execution/script [2018-12-05 09:58:16,02] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:1:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-spr/shard-1/execution/script [2018-12-05 09:58:16,03] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:2:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-2/execution/script [2018-12-05 09:58:16,04] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:0:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-0/execution/script [2018-12-05 09:58:16,05] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:1:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-macs2/shard-1/execution/script [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:0:1]: job id: 29050 [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:2:1]: job id: 29054 [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.pool_ta:NA:1]: job id: 29061 [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:1:1]: job id: 29100 [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:1:1]: job id: 29069 [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:0:1]: job id: 29097 [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:2:1]: job id: 29071 [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:1:1]: Status change from - to WaitingForReturnCodeFile [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.pool_ta:NA:1]: Status change from - to Done [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:2:1]: Status change from - to Done [2018-12-05 09:58:19,34] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:2:1]: Status change from - to WaitingForReturnCodeFile [2018-12-05 09:58:19,35] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:1:1]: Status change from - to Done [2018-12-05 09:58:19,35] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.spr:0:1]: Status change from - to Done [2018-12-05 09:58:19,35] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:0:1]: Status change from - to WaitingForReturnCodeFile [2018-12-05 09:58:21,45] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:1:1]: Status change from WaitingForReturnCodeFile to Done [2018-12-05 09:58:21,88] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:2:1]: Status change from WaitingForReturnCodeFile to Done [2018-12-05 09:58:29,98] [info] BackgroundConfigAsyncJobExecutionActor [6155fd91atac.macs2:0:1]: Status change from WaitingForReturnCodeFile to Done [2018-12-05 09:58:30,10] [error] WorkflowManagerActor Workflow 6155fd91-835b-4644-b8d5-c4a8642a3263 failed (during ExecutingWorkflowState): Job atac.spr:1:1 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: /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-spr/shard-1/execution/stderr. Traceback (most recent call last): File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_spr.py", line 130, in main() File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_spr.py", line 125, in main assert_file_not_empty(ta_pr2) File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 176, in assert_file_not_empty raise Exception('File is empty ({}). Help: {}'.format(f,help)) Exception: File is empty (KJ065_R1_TRIM.trim.nodup.tn5.pr2.tagAlign.gz). Help: Job atac.spr:2:1 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: /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-spr/shard-2/execution/stderr. Traceback (most recent call last): File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_spr.py", line 130, in main() File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_spr.py", line 125, in main assert_file_not_empty(ta_pr2) File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 176, in assert_file_not_empty raise Exception('File is empty ({}). Help: {}'.format(f,help)) Exception: File is empty (KJ066_R1_TRIM.trim.nodup.tn5.pr2.tagAlign.gz). Help: Job atac.spr:0:1 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: /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/6155fd91-835b-4644-b8d5-c4a8642a3263/call-spr/shard-0/execution/stderr. Traceback (most recent call last): File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_spr.py", line 130, in main() File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_spr.py", line 125, in main assert_file_not_empty(ta_pr2) File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 176, in assert_file_not_empty raise Exception('File is empty ({}). Help: {}'.format(f,help)) Exception: File is empty (KJ064_R1_TRIM.trim.nodup.tn5.pr2.tagAlign.gz). Help: [2018-12-05 09:58:30,10] [info] WorkflowManagerActor WorkflowActor-6155fd91-835b-4644-b8d5-c4a8642a3263 is in a terminal state: WorkflowFailedState [2018-12-05 09:58:56,89] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'. [2018-12-05 09:58:59,35] [info] Workflow polling stopped [2018-12-05 09:58:59,36] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds [2018-12-05 09:58:59,37] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds [2018-12-05 09:58:59,37] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds [2018-12-05 09:58:59,37] [info] Aborting all running workflows. [2018-12-05 09:58:59,37] [info] JobExecutionTokenDispenser stopped [2018-12-05 09:58:59,37] [info] WorkflowStoreActor stopped [2018-12-05 09:58:59,37] [info] WorkflowLogCopyRouter stopped [2018-12-05 09:58:59,37] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds [2018-12-05 09:58:59,38] [info] WorkflowManagerActor All workflows finished [2018-12-05 09:58:59,38] [info] WorkflowManagerActor stopped [2018-12-05 09:58:59,38] [info] Connection pools shut down [2018-12-05 09:58:59,38] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds [2018-12-05 09:58:59,38] [info] Shutting down JobStoreActor - Timeout = 1800 seconds [2018-12-05 09:58:59,38] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds [2018-12-05 09:58:59,38] [info] SubWorkflowStoreActor stopped [2018-12-05 09:58:59,38] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds [2018-12-05 09:58:59,38] [info] Shutting down DockerHashActor - Timeout = 1800 seconds [2018-12-05 09:58:59,38] [info] Shutting down IoProxy - Timeout = 1800 seconds [2018-12-05 09:58:59,38] [info] CallCacheWriteActor Shutting down: 0 queued messages to process [2018-12-05 09:58:59,38] [info] WriteMetadataActor Shutting down: 0 queued messages to process [2018-12-05 09:58:59,38] [info] KvWriteActor Shutting down: 0 queued messages to process [2018-12-05 09:58:59,38] [info] JobStoreActor stopped [2018-12-05 09:58:59,38] [info] DockerHashActor stopped [2018-12-05 09:58:59,38] [info] IoProxy stopped [2018-12-05 09:58:59,38] [info] CallCacheWriteActor stopped [2018-12-05 09:58:59,38] [info] ServiceRegistryActor stopped [2018-12-05 09:58:59,40] [info] Database closed [2018-12-05 09:58:59,40] [info] Stream materializer shut down Workflow 6155fd91-835b-4644-b8d5-c4a8642a3263 transitioned to state Failed [2018-12-05 09:58:59,43] [info] Automatic shutdown of the async connection [2018-12-05 09:58:59,44] [info] Gracefully shutdown sentry threads. [2018-12-05 09:58:59,44] [info] Shutdown finished.