/netapp/home/kirsty.jamieson/.bash_profile: line 7: syntax error: unexpected end of file Picked up _JAVA_OPTIONS: -Xms256M -Xmx16384M -XX:ParallelGCThreads=1 [2018-11-27 13:08:35,73] [info] Running with database db.url = jdbc:hsqldb:mem:9b5b8bab-c392-4c22-9ae8-c26c9797a3e0;shutdown=false;hsqldb.tx=mvcc [2018-11-27 13:08:53,90] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000 [2018-11-27 13:08:53,92] [info] [RenameWorkflowOptionsInMetadata] 100% [2018-11-27 13:08:54,12] [info] Running with database db.url = jdbc:hsqldb:mem:7dd902dc-1480-4d53-ae1c-0ca2afc1153a;shutdown=false;hsqldb.tx=mvcc [2018-11-27 13:08:54,62] [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 [2018-11-27 13:08:54,65] [warn] Couldn't find a suitable DSN, defaulting to a Noop one. [2018-11-27 13:08:54,66] [info] Using noop to send events. [2018-11-27 13:08:55,08] [info] Slf4jLogger started [2018-11-27 13:08:55,33] [info] Workflow heartbeat configuration: { "cromwellId" : "cromid-54e28ff", "heartbeatInterval" : "2 minutes", "ttl" : "10 minutes", "writeBatchSize" : 10000, "writeThreshold" : 10000 } [2018-11-27 13:08:55,37] [info] Metadata summary refreshing every 2 seconds. [2018-11-27 13:08:55,42] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. [2018-11-27 13:08:55,43] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. [2018-11-27 13:08:55,43] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. [2018-11-27 13:08:56,29] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. [2018-11-27 13:08:56,32] [info] JES batch polling interval is 33333 milliseconds [2018-11-27 13:08:56,32] [info] JES batch polling interval is 33333 milliseconds [2018-11-27 13:08:56,32] [info] SingleWorkflowRunnerActor: Version 34 [2018-11-27 13:08:56,32] [info] JES batch polling interval is 33333 milliseconds [2018-11-27 13:08:56,32] [info] PAPIQueryManager Running with 3 workers [2018-11-27 13:08:56,33] [info] SingleWorkflowRunnerActor: Submitting workflow [2018-11-27 13:08:56,38] [info] Unspecified type (Unspecified version) workflow a7b66b90-77f3-47b9-afa6-d874bd8e21ab submitted [2018-11-27 13:08:56,44] [info] SingleWorkflowRunnerActor: Workflow submitted a7b66b90-77f3-47b9-afa6-d874bd8e21ab [2018-11-27 13:08:56,45] [info] 1 new workflows fetched [2018-11-27 13:08:56,45] [info] WorkflowManagerActor Starting workflow a7b66b90-77f3-47b9-afa6-d874bd8e21ab [2018-11-27 13:08:56,45] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData [2018-11-27 13:08:56,46] [info] WorkflowManagerActor Successfully started WorkflowActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [2018-11-27 13:08:56,46] [info] Retrieved 1 workflows from the WorkflowStoreActor [2018-11-27 13:08:56,47] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. [2018-11-27 13:08:56,57] [info] MaterializeWorkflowDescriptorActor [a7b66b90]: Parsing workflow as WDL draft-2 [2018-11-27 13:09:22,32] [info] MaterializeWorkflowDescriptorActor [a7b66b90]: Call-to-Backend assignments: atac.overlap_ppr -> Local, atac.macs2_ppr2 -> Local, atac.reproducibility_idr -> Local, atac.pool_ta_pr2 -> Local, atac.ataqc -> Local, atac.spr -> Local, atac.filter -> Local, atac.macs2_ppr1 -> Local, atac.bowtie2 -> Local, atac.macs2_pooled -> Local, atac.pool_ta -> Local, atac.trim_adapter -> Local, atac.xcor -> Local, atac.idr -> Local, atac.pool_ta_pr1 -> Local, atac.reproducibility_overlap -> Local, atac.macs2_pr2 -> Local, atac.read_genome_tsv -> Local, atac.overlap -> Local, atac.macs2 -> Local, atac.overlap_pr -> Local, atac.macs2_pr1 -> Local, atac.bam2ta -> Local, atac.idr_pr -> Local, atac.qc_report -> Local, atac.idr_ppr -> Local [2018-11-27 13:09:22,44] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,45] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,45] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,45] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,45] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,45] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,45] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,45] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,45] [warn] Local [a7b66b90]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,45] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,45] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,46] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,47] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,47] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,47] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:22,47] [warn] Local [a7b66b90]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2018-11-27 13:09:24,80] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Starting atac.read_genome_tsv [2018-11-27 13:09:24,80] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Condition met: 'enable_idr'. Running conditional section [2018-11-27 13:09:24,80] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Condition met: '!true_rep_only'. Running conditional section [2018-11-27 13:09:24,81] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Condition met: '!align_only && !true_rep_only && enable_idr'. Running conditional section [2018-11-27 13:09:24,81] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Condition met: 'enable_xcor'. Running conditional section [2018-11-27 13:09:24,81] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Condition met: '!align_only && !true_rep_only'. Running conditional section [2018-11-27 13:09:24,81] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Condition met: 'enable_idr'. Running conditional section [2018-11-27 13:09:25,43] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.read_genome_tsv:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:09:25,79] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.read_genome_tsv:NA:1]: cat /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-read_genome_tsv/inputs/-1224684285/hg38_local.tsv [2018-11-27 13:09:25,85] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.read_genome_tsv:NA:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-read_genome_tsv/execution/script [2018-11-27 13:09:30,47] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.read_genome_tsv:NA:1]: job id: 26408 [2018-11-27 13:09:30,48] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.read_genome_tsv:NA:1]: Status change from - to Done [2018-11-27 13:09:37,10] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Starting atac.bam2ta (3 shards) [2018-11-27 13:09:37,31] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:09:37,32] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:09:37,32] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:2:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:09:37,35] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:1:1]: python $(which encode_bam2ta.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-bam2ta/shard-1/inputs/-1239304995/KJ065_R1_TRIM.trim.nodup.bam \ --paired-end \ \ --regex-grep-v-ta 'chrM' \ --subsample 0 \ --nth 2 [2018-11-27 13:09:37,35] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:0:1]: python $(which encode_bam2ta.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-bam2ta/shard-0/inputs/-1239304996/KJ064_R1_TRIM.trim.nodup.bam \ --paired-end \ \ --regex-grep-v-ta 'chrM' \ --subsample 0 \ --nth 2 [2018-11-27 13:09:37,35] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:2:1]: python $(which encode_bam2ta.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-bam2ta/shard-2/inputs/-1239304994/KJ066_R1_TRIM.trim.nodup.bam \ --paired-end \ \ --regex-grep-v-ta 'chrM' \ --subsample 0 \ --nth 2 [2018-11-27 13:09:37,37] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:2:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-bam2ta/shard-2/execution/script [2018-11-27 13:09:37,37] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:0:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-bam2ta/shard-0/execution/script [2018-11-27 13:09:37,37] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:1:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-bam2ta/shard-1/execution/script [2018-11-27 13:09:40,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:2:1]: job id: 26476 [2018-11-27 13:09:40,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:1:1]: job id: 26477 [2018-11-27 13:09:40,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:0:1]: job id: 26478 [2018-11-27 13:09:40,47] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:1:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:09:40,47] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:0:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:09:40,47] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:2:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:19:38,38] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:2:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:21:50,70] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:1:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:27:57,87] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.bam2ta:0:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:01,92] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Condition met: '!true_rep_only && length(tas_) > 1'. Running conditional section [2018-11-27 13:28:01,92] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Condition met: 'length(tas_) > 1'. Running conditional section [2018-11-27 13:28:04,05] [info] WorkflowExecutionActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab [a7b66b90]: Starting atac.spr (3 shards), atac.xcor (3 shards), atac.macs2 (3 shards), atac.pool_ta [2018-11-27 13:28:04,31] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:28:04,31] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:2:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:28:04,31] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:2:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:28:04,31] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:28:04,31] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:28:04,31] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:28:04,31] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:28:04,32] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:28:04,32] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.pool_ta:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:28:04,32] [warn] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:2:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory [2018-11-27 13:28:04,34] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:2:1]: python $(which encode_xcor.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-2/inputs/678337650/KJ066_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --paired-end \ --subsample 25000000 \ --speak=0 \ --nth 2 [2018-11-27 13:28:04,34] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:0:1]: python $(which encode_spr.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-spr/shard-0/inputs/693856368/KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --paired-end [2018-11-27 13:28:04,34] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:1:1]: python $(which encode_spr.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-spr/shard-1/inputs/686097009/KJ065_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --paired-end [2018-11-27 13:28:04,35] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:0:1]: python $(which encode_macs2_atac.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-0/inputs/693856368/KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --gensz hs \ --chrsz /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-0/inputs/-2107835088/hg38.chrom.sizes \ --cap-num-peak 300000 \ --pval-thresh 0.01 \ --smooth-win 73 \ --make-signal \ \ --blacklist /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-0/inputs/-2107835088/hg38.blacklist.bed.gz # ugly part to deal with optional outputs with Google JES backend touch null [2018-11-27 13:28:04,36] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:1:1]: python $(which encode_xcor.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-1/inputs/686097009/KJ065_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --paired-end \ --subsample 25000000 \ --speak=0 \ --nth 2 [2018-11-27 13:28:04,36] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:0:1]: python $(which encode_xcor.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-0/inputs/693856368/KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --paired-end \ --subsample 25000000 \ --speak=0 \ --nth 2 [2018-11-27 13:28:04,36] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:2:1]: python $(which encode_spr.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-spr/shard-2/inputs/678337650/KJ066_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --paired-end [2018-11-27 13:28:04,36] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:0:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-spr/shard-0/execution/script [2018-11-27 13:28:04,37] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:2:1]: python $(which encode_macs2_atac.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-2/inputs/678337650/KJ066_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --gensz hs \ --chrsz /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-2/inputs/-2107835088/hg38.chrom.sizes \ --cap-num-peak 300000 \ --pval-thresh 0.01 \ --smooth-win 73 \ --make-signal \ \ --blacklist /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-2/inputs/-2107835088/hg38.blacklist.bed.gz # ugly part to deal with optional outputs with Google JES backend touch null [2018-11-27 13:28:04,37] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:2:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-2/execution/script [2018-11-27 13:28:04,38] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:1:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-spr/shard-1/execution/script [2018-11-27 13:28:04,38] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:0:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-0/execution/script [2018-11-27 13:28:04,38] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:1:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-1/execution/script [2018-11-27 13:28:04,39] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:2:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-spr/shard-2/execution/script [2018-11-27 13:28:04,39] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:0:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-0/execution/script [2018-11-27 13:28:04,39] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:2:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-2/execution/script [2018-11-27 13:28:04,40] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:1:1]: python $(which encode_macs2_atac.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-1/inputs/686097009/KJ065_R1_TRIM.trim.nodup.tn5.tagAlign.gz \ --gensz hs \ --chrsz /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-1/inputs/-2107835088/hg38.chrom.sizes \ --cap-num-peak 300000 \ --pval-thresh 0.01 \ --smooth-win 73 \ --make-signal \ \ --blacklist /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-1/inputs/-2107835088/hg38.blacklist.bed.gz # ugly part to deal with optional outputs with Google JES backend touch null [2018-11-27 13:28:04,40] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.pool_ta:NA:1]: python $(which encode_pool_ta.py) \ /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-pool_ta/inputs/693856368/KJ064_R1_TRIM.trim.nodup.tn5.tagAlign.gz /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-pool_ta/inputs/686097009/KJ065_R1_TRIM.trim.nodup.tn5.tagAlign.gz /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-pool_ta/inputs/678337650/KJ066_R1_TRIM.trim.nodup.tn5.tagAlign.gz [2018-11-27 13:28:04,42] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.pool_ta:NA:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-pool_ta/execution/script [2018-11-27 13:28:04,44] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:1:1]: executing: /bin/bash /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-macs2/shard-1/execution/script [2018-11-27 13:28:05,45] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:0:1]: job id: 28224 [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:1:1]: job id: 28235 [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:0:1]: job id: 28238 [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:2:1]: job id: 28231 [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:1:1]: job id: 28269 [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:2:1]: job id: 28277 [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:1:1]: job id: 28318 [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:2:1]: job id: 28271 [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.pool_ta:NA:1]: job id: 28308 [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.pool_ta:NA:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:2:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:0:1]: job id: 28280 [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:1:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:1:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:0:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:0:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:0:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:2:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:2:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:28:05,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:1:1]: Status change from - to WaitingForReturnCodeFile [2018-11-27 13:28:11,41] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.pool_ta:NA:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:12,49] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:1:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:13,46] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:2:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:13,50] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:1:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:13,56] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.spr:0:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:14,32] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:2:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:15,04] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.xcor:0:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:16,26] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:1:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:16,82] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:2:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:29,80] [info] BackgroundConfigAsyncJobExecutionActor [a7b66b90atac.macs2:0:1]: Status change from WaitingForReturnCodeFile to Done [2018-11-27 13:28:30,59] [error] WorkflowManagerActor Workflow a7b66b90-77f3-47b9-afa6-d874bd8e21ab failed (during ExecutingWorkflowState): 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/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/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.xcor: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/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-0/execution/stderr. Traceback (most recent call last): File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 99, in main() File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 88, in main ta_subsampled, args.speak, args.nth, args.out_dir) File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 53, in xcor run_shell_cmd(cmd1) File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 263, in run_shell_cmd pid, pgid, cmd, ret)) Exception: Killed PID=28424, PGID=28424 CMD=Rscript --max-ppsize=500000 $(which run_spp.R) -rf -c=KJ064_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign.gz -p=2 -filtchr=chrM -savp=KJ064_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.plot.pdf -out=KJ064_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.qc -speak=0 STDOUT=################ ChIP data: KJ064_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign.gz Control data: NA strandshift(min): -500 strandshift(step): 5 strandshift(max) 1500 user-defined peak shift 0 exclusion(min): 10 exclusion(max): NaN num parallel nodes: 2 FDR threshold: 0.01 NumPeaks Threshold: NA Output Directory: . narrowPeak output file name: NA regionPeak output file name: NA Rdata filename: NA plot pdf filename: KJ064_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.plot.pdf result filename: KJ064_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.qc Overwrite files?: TRUE Decompressing ChIP file Loading required package: caTools Reading ChIP tagAlign/BAM file KJ064_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign.gz opened /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-0/tmp.e4b6e8bb/RtmpGMzjpk/KJ064_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign6f0816242e20 done. read 1 fragments ChIP data read length 47 [1] TRUE Calculating peak characteristics Warning message: In max(ccl.av$x[ccl.av$y >= th]) : no non-missing arguments to max; returning -Inf Minimum cross-correlation value NaN Minimum cross-correlation shift 1500 Error in approx(crosscorr$cross.correlation$x, crosscorr$cross.correlation$y, : need at least two non-NA values to interpolate Execution halted Job atac.xcor: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/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-2/execution/stderr. Traceback (most recent call last): File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 99, in main() File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 88, in main ta_subsampled, args.speak, args.nth, args.out_dir) File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 53, in xcor run_shell_cmd(cmd1) File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 263, in run_shell_cmd pid, pgid, cmd, ret)) Exception: Killed PID=28423, PGID=28423 CMD=Rscript --max-ppsize=500000 $(which run_spp.R) -rf -c=KJ066_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign.gz -p=2 -filtchr=chrM -savp=KJ066_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.plot.pdf -out=KJ066_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.qc -speak=0 STDOUT=################ ChIP data: KJ066_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign.gz Control data: NA strandshift(min): -500 strandshift(step): 5 strandshift(max) 1500 user-defined peak shift 0 exclusion(min): 10 exclusion(max): NaN num parallel nodes: 2 FDR threshold: 0.01 NumPeaks Threshold: NA Output Directory: . narrowPeak output file name: NA regionPeak output file name: NA Rdata filename: NA plot pdf filename: KJ066_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.plot.pdf result filename: KJ066_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.qc Overwrite files?: TRUE Decompressing ChIP file Loading required package: caTools Reading ChIP tagAlign/BAM file KJ066_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign.gz opened /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-2/tmp.70eb4852/RtmpzXgfpk/KJ066_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign6f07203c1eaf done. read 1 fragments ChIP data read length 47 [1] TRUE Calculating peak characteristics Warning message: In max(ccl.av$x[ccl.av$y >= th]) : no non-missing arguments to max; returning -Inf Minimum cross-correlation value NaN Minimum cross-correlation shift 1500 Error in approx(crosscorr$cross.correlation$x, crosscorr$cross.correlation$y, : need at least two non-NA values to interpolate Execution halted 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/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/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: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/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/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: Job atac.xcor: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/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-1/execution/stderr. Traceback (most recent call last): File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 99, in main() File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 88, in main ta_subsampled, args.speak, args.nth, args.out_dir) File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 53, in xcor run_shell_cmd(cmd1) File "/netapp/home/kirsty.jamieson/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 263, in run_shell_cmd pid, pgid, cmd, ret)) Exception: Killed PID=28425, PGID=28425 CMD=Rscript --max-ppsize=500000 $(which run_spp.R) -rf -c=KJ065_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign.gz -p=2 -filtchr=chrM -savp=KJ065_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.plot.pdf -out=KJ065_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.qc -speak=0 STDOUT=################ ChIP data: KJ065_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign.gz Control data: NA strandshift(min): -500 strandshift(step): 5 strandshift(max) 1500 user-defined peak shift 0 exclusion(min): 10 exclusion(max): NaN num parallel nodes: 2 FDR threshold: 0.01 NumPeaks Threshold: NA Output Directory: . narrowPeak output file name: NA regionPeak output file name: NA Rdata filename: NA plot pdf filename: KJ065_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.plot.pdf result filename: KJ065_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.cc.qc Overwrite files?: TRUE Decompressing ChIP file Loading required package: caTools Reading ChIP tagAlign/BAM file KJ065_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign.gz opened /scrapp/kirsty.jamieson/atac-seq-pipeline/cromwell-executions/atac/a7b66b90-77f3-47b9-afa6-d874bd8e21ab/call-xcor/shard-1/tmp.1a10ea0d/RtmpNFOjpk/KJ065_R1_TRIM.trim.nodup.tn5.no_chrM.R1.25M.tagAlign6f09295e4570 done. read 1 fragments ChIP data read length 46 [1] TRUE Calculating peak characteristics Warning message: In max(ccl.av$x[ccl.av$y >= th]) : no non-missing arguments to max; returning -Inf Minimum cross-correlation value NaN Minimum cross-correlation shift 1500 Error in approx(crosscorr$cross.correlation$x, crosscorr$cross.correlation$y, : need at least two non-NA values to interpolate Execution halted [2018-11-27 13:28:30,60] [info] WorkflowManagerActor WorkflowActor-a7b66b90-77f3-47b9-afa6-d874bd8e21ab is in a terminal state: WorkflowFailedState [2018-11-27 13:29:06,13] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'. [2018-11-27 13:29:10,45] [info] Workflow polling stopped [2018-11-27 13:29:10,46] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds [2018-11-27 13:29:10,46] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds [2018-11-27 13:29:10,47] [info] Aborting all running workflows. [2018-11-27 13:29:10,47] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds [2018-11-27 13:29:10,47] [info] JobExecutionTokenDispenser stopped [2018-11-27 13:29:10,47] [info] WorkflowStoreActor stopped [2018-11-27 13:29:10,47] [info] WorkflowLogCopyRouter stopped [2018-11-27 13:29:10,47] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds [2018-11-27 13:29:10,47] [info] WorkflowManagerActor All workflows finished [2018-11-27 13:29:10,47] [info] WorkflowManagerActor stopped [2018-11-27 13:29:10,47] [info] Connection pools shut down [2018-11-27 13:29:10,47] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds [2018-11-27 13:29:10,47] [info] Shutting down JobStoreActor - Timeout = 1800 seconds [2018-11-27 13:29:10,47] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds [2018-11-27 13:29:10,47] [info] SubWorkflowStoreActor stopped [2018-11-27 13:29:10,47] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds [2018-11-27 13:29:10,47] [info] Shutting down DockerHashActor - Timeout = 1800 seconds [2018-11-27 13:29:10,47] [info] Shutting down IoProxy - Timeout = 1800 seconds [2018-11-27 13:29:10,47] [info] CallCacheWriteActor Shutting down: 0 queued messages to process [2018-11-27 13:29:10,47] [info] JobStoreActor stopped [2018-11-27 13:29:10,47] [info] KvWriteActor Shutting down: 0 queued messages to process [2018-11-27 13:29:10,47] [info] CallCacheWriteActor stopped [2018-11-27 13:29:10,47] [info] WriteMetadataActor Shutting down: 0 queued messages to process [2018-11-27 13:29:10,47] [info] DockerHashActor stopped [2018-11-27 13:29:10,47] [info] IoProxy stopped [2018-11-27 13:29:10,48] [info] ServiceRegistryActor stopped [2018-11-27 13:29:10,50] [info] Database closed [2018-11-27 13:29:10,50] [info] Stream materializer shut down Workflow a7b66b90-77f3-47b9-afa6-d874bd8e21ab transitioned to state Failed [2018-11-27 13:29:10,53] [info] Automatic shutdown of the async connection [2018-11-27 13:29:10,53] [info] Gracefully shutdown sentry threads. [2018-11-27 13:29:10,54] [info] Shutdown finished.