Script started on 2018-11-30 14:26:20-0500
goldrath@Goldrath-vbox:~/Documents/ATACPipeline/atac-seq-pipeline$ source activate encode-atac-seq-pipeline
(encode-atac-seq-pipeline) goldrath@Goldrath-vbox:~/Documents/ATACPipeline/atac-seq-pipeline$ INPUT=examples/local/ENCSR356KRQ_subsampled.json
(encode-atac-seq-pipeline) goldrath@Goldrath-vbox:~/Documents/ATACPipeline/atac-seq-pipeline$ java -jar -Dconfig.file=backends/backend.conf cromwell-34.jar run atac.wdl -i ${INPUT}
[2018-11-30 14:27:10,83] [info] Running with database db.url = jdbc:hsqldb:mem:6cb154d3-fca0-4a19-8a45-a984a71c8f67;shutdown=false;hsqldb.tx=mvcc
[2018-11-30 14:27:21,75] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-11-30 14:27:21,77] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-11-30 14:27:21,92] [info] Running with database db.url = jdbc:hsqldb:mem:b67e6b5f-ce23-4f08-9f59-0159705f4b8f;shutdown=false;hsqldb.tx=mvcc
[2018-11-30 14:27:22,31] [[38;5;220mwarn[0m] 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
[2018-11-30 14:27:22,34] [[38;5;220mwarn[0m] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-11-30 14:27:22,34] [info] Using noop to send events.
[2018-11-30 14:27:22,69] [info] Slf4jLogger started
[2018-11-30 14:27:22,92] [info] Workflow heartbeat configuration:
{
  "cromwellId" : "cromid-ac8a7dd",
  "heartbeatInterval" : "2 minutes",
  "ttl" : "10 minutes",
  "writeBatchSize" : 10000,
  "writeThreshold" : 10000
}
[2018-11-30 14:27:22,97] [info] Metadata summary refreshing every 2 seconds.
[2018-11-30 14:27:23,07] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-11-30 14:27:23,08] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-11-30 14:27:23,08] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2018-11-30 14:27:23,79] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2018-11-30 14:27:23,83] [info] SingleWorkflowRunnerActor: Version 34
[2018-11-30 14:27:23,84] [info] JES batch polling interval is 33333 milliseconds
[2018-11-30 14:27:23,84] [info] JES batch polling interval is 33333 milliseconds
[2018-11-30 14:27:23,84] [info] JES batch polling interval is 33333 milliseconds
[2018-11-30 14:27:23,84] [info] PAPIQueryManager Running with 3 workers
[2018-11-30 14:27:23,85] [info] SingleWorkflowRunnerActor: Submitting workflow
[2018-11-30 14:27:23,91] [info] Unspecified type (Unspecified version) workflow 7a43f040-d436-4dbc-9596-8fbbccfa2827 submitted
[2018-11-30 14:27:24,00] [info] SingleWorkflowRunnerActor: Workflow submitted [38;5;2m7a43f040-d436-4dbc-9596-8fbbccfa2827[0m
[2018-11-30 14:27:24,01] [info] 1 new workflows fetched
[2018-11-30 14:27:24,01] [[38;5;220mwarn[0m] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData
[2018-11-30 14:27:24,02] [info] WorkflowManagerActor Starting workflow [38;5;2m7a43f040-d436-4dbc-9596-8fbbccfa2827[0m
[2018-11-30 14:27:24,02] [info] WorkflowManagerActor Successfully started WorkflowActor-7a43f040-d436-4dbc-9596-8fbbccfa2827
[2018-11-30 14:27:24,03] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2018-11-30 14:27:24,04] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2018-11-30 14:27:24,14] [info] MaterializeWorkflowDescriptorActor [[38;5;2m7a43f040[0m]: Parsing workflow as WDL draft-2
[2018-11-30 14:27:39,89] [info] MaterializeWorkflowDescriptorActor [[38;5;2m7a43f040[0m]: Call-to-Backend assignments: atac.filter -> Local, atac.macs2_ppr1 -> Local, atac.reproducibility_overlap -> Local, atac.macs2 -> Local, atac.pool_ta_pr2 -> Local, atac.ataqc -> Local, atac.macs2_pooled -> Local, atac.macs2_pr1 -> Local, atac.spr -> Local, atac.trim_adapter -> Local, atac.idr_pr -> Local, atac.bowtie2 -> Local, atac.reproducibility_idr -> Local, atac.read_genome_tsv -> Local, atac.pool_ta_pr1 -> Local, atac.overlap_pr -> Local, atac.xcor -> Local, atac.overlap -> Local, atac.overlap_ppr -> Local, atac.macs2_pr2 -> Local, atac.qc_report -> Local, atac.pool_ta -> Local, atac.bam2ta -> Local, atac.idr -> Local, atac.idr_ppr -> Local, atac.macs2_ppr2 -> Local
[2018-11-30 14:27:40,03] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,03] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,03] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,03] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,04] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,04] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,04] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,05] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,05] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,06] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,07] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:40,07] [[38;5;220mwarn[0m] Local [[38;5;2m7a43f040[0m]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-30 14:27:42,32] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Starting atac.read_genome_tsv
[2018-11-30 14:27:42,32] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Condition met: 'enable_xcor'. Running conditional section
[2018-11-30 14:27:42,32] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Condition met: '!true_rep_only'. Running conditional section
[2018-11-30 14:27:42,32] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Condition met: 'enable_idr'. Running conditional section
[2018-11-30 14:27:42,32] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Condition met: 'enable_idr'. Running conditional section
[2018-11-30 14:27:42,32] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Condition met: '!align_only && !true_rep_only'. Running conditional section
[2018-11-30 14:27:42,33] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Condition met: '!align_only && !true_rep_only && enable_idr'. Running conditional section
[2018-11-30 14:27:42,89] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.read_genome_tsv:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-30 14:27:43,12] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.read_genome_tsv:NA:1]: [38;5;5mcat /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-read_genome_tsv/inputs/498158547/hg38_local.tsv[0m
[2018-11-30 14:27:43,18] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.read_genome_tsv:NA:1]: executing: /bin/bash /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-read_genome_tsv/execution/script
[2018-11-30 14:27:46,47] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Starting atac.trim_adapter (2 shards)
[2018-11-30 14:27:46,81] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-30 14:27:46,81] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-30 14:27:46,84] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:0:1]: [38;5;5mpython $(which encode_trim_adapter.py) \
	/home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-trim_adapter/shard-0/execution/write_tsv_1a2bc0caecc3233fe2760cedc6b09098.tmp \
	--adapters /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-trim_adapter/shard-0/execution/write_tsv_d41d8cd98f00b204e9800998ecf8427e.tmp \
	--paired-end \
	--auto-detect-adapter \
	--min-trim-len 5 \
	--err-rate 0.1 \
	--nth 2[0m
[2018-11-30 14:27:46,84] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:1:1]: [38;5;5mpython $(which encode_trim_adapter.py) \
	/home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-trim_adapter/shard-1/execution/write_tsv_ee47ae51718be79a6e8f937dc90c96dc.tmp \
	--adapters /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-trim_adapter/shard-1/execution/write_tsv_d41d8cd98f00b204e9800998ecf8427e.tmp \
	--paired-end \
	--auto-detect-adapter \
	--min-trim-len 5 \
	--err-rate 0.1 \
	--nth 2[0m
[2018-11-30 14:27:46,85] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:1:1]: executing: /bin/bash /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-trim_adapter/shard-1/execution/script
[2018-11-30 14:27:46,85] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:0:1]: executing: /bin/bash /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-trim_adapter/shard-0/execution/script
[2018-11-30 14:27:48,15] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:0:1]: job id: 28268
[2018-11-30 14:27:48,15] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.read_genome_tsv:NA:1]: job id: 28244
[2018-11-30 14:27:48,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:1:1]: job id: 28271
[2018-11-30 14:27:48,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:1:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-30 14:27:48,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-30 14:27:48,16] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.read_genome_tsv:NA:1]: Status change from - to Done
[2018-11-30 14:28:06,20] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-30 14:28:07,88] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Starting atac.bowtie2
[2018-11-30 14:28:08,80] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:0:1]: Unrecognized runtime attribute keys: preemptible, disks, cpu, time, memory
[2018-11-30 14:28:08,81] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:0:1]: [38;5;5mpython $(which encode_bowtie2.py) \
	/home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-bowtie2/shard-0/inputs/-985136688/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.tar \
	/home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-bowtie2/shard-0/inputs/1331069709/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.fastq.gz /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-bowtie2/shard-0/inputs/1331069709/merge_fastqs_R2_ENCFF248EJF.subsampled.400.trim.merged.fastq.gz \
	--paired-end \
	--multimapping 4 \
	 \
	--nth 1[0m
[2018-11-30 14:28:08,82] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:0:1]: executing: /bin/bash /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-bowtie2/shard-0/execution/script
[2018-11-30 14:28:11,51] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.trim_adapter:1:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-30 14:28:12,97] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Starting atac.bowtie2
[2018-11-30 14:28:13,10] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:0:1]: job id: 28412
[2018-11-30 14:28:13,10] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-30 14:28:13,83] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:1:1]: Unrecognized runtime attribute keys: preemptible, disks, cpu, time, memory
[2018-11-30 14:28:13,83] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:1:1]: [38;5;5mpython $(which encode_bowtie2.py) \
	/home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-bowtie2/shard-1/inputs/-985136688/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.tar \
	/home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-bowtie2/shard-1/inputs/1323310350/merge_fastqs_R1_ENCFF641SFZ.subsampled.400.trim.merged.fastq.gz /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-bowtie2/shard-1/inputs/1323310350/merge_fastqs_R2_ENCFF031ARQ.subsampled.400.trim.merged.fastq.gz \
	--paired-end \
	--multimapping 4 \
	 \
	--nth 1[0m
[2018-11-30 14:28:13,83] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:1:1]: executing: /bin/bash /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-bowtie2/shard-1/execution/script
[2018-11-30 14:28:18,11] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:1:1]: job id: 28435
[2018-11-30 14:28:18,11] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:1:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-30 14:35:59,60] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-30 14:37:46,73] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.bowtie2:1:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-30 14:37:52,21] [info] WorkflowExecutionActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 [[38;5;2m7a43f040[0m]: Starting atac.filter (2 shards)
[2018-11-30 14:37:52,81] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-30 14:37:52,81] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-30 14:37:52,81] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:0:1]: [38;5;5mpython $(which encode_filter.py) \
	/home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-filter/shard-0/inputs/-1518532740/ENCFF341MYG.subsampled.400.trim.merged.bam \
	--paired-end \
	--multimapping 4 \
	--dup-marker picard \
	--mapq-thresh 30 \
	 \
	--nth 1
# ugly part to deal with optional outputs with Google JES backend

touch null[0m
[2018-11-30 14:37:52,81] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:1:1]: [38;5;5mpython $(which encode_filter.py) \
	/home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-filter/shard-1/inputs/-1526292099/ENCFF641SFZ.subsampled.400.trim.merged.bam \
	--paired-end \
	--multimapping 4 \
	--dup-marker picard \
	--mapq-thresh 30 \
	 \
	--nth 1
# ugly part to deal with optional outputs with Google JES backend

touch null[0m
[2018-11-30 14:37:52,82] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:1:1]: executing: /bin/bash /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-filter/shard-1/execution/script
[2018-11-30 14:37:52,83] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:0:1]: executing: /bin/bash /home/goldrath/Documents/ATACPipeline/atac-seq-pipeline/cromwell-executions/atac/7a43f040-d436-4dbc-9596-8fbbccfa2827/call-filter/shard-0/execution/script
[2018-11-30 14:37:53,11] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:1:1]: job id: 28792
[2018-11-30 14:37:53,11] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:0:1]: job id: 28802
[2018-11-30 14:37:53,13] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:1:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-30 14:37:53,13] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-30 14:38:57,36] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:1:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-30 14:39:07,57] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m7a43f040[0matac.filter:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-30 14:39:08,58] [[38;5;1merror[0m] WorkflowManagerActor Workflow 7a43f040-d436-4dbc-9596-8fbbccfa2827 failed (during ExecutingWorkflowState): cromwell.backend.standard.StandardAsyncExecutionActor$$anon$2: Failed to evaluate job outputs:
Bad output 'filter.flagstat_qc': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'filter.dup_qc': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'filter.pbc_qc': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'filter.mito_dup_log': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$handleExecutionSuccess$1(StandardAsyncExecutionActor.scala:839)
	at scala.util.Success.$anonfun$map$1(Try.scala:251)
	at scala.util.Success.map(Try.scala:209)
	at scala.concurrent.Future.$anonfun$map$1(Future.scala:288)
	at scala.concurrent.impl.Promise.liftedTree1$1(Promise.scala:29)
	at scala.concurrent.impl.Promise.$anonfun$transform$1(Promise.scala:29)
	at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:60)
	at akka.dispatch.BatchingExecutor$AbstractBatch.processBatch(BatchingExecutor.scala:55)
	at akka.dispatch.BatchingExecutor$BlockableBatch.$anonfun$run$1(BatchingExecutor.scala:91)
	at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:12)
	at scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:81)
	at akka.dispatch.BatchingExecutor$BlockableBatch.run(BatchingExecutor.scala:91)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

[2018-11-30 14:39:08,58] [info] WorkflowManagerActor WorkflowActor-7a43f040-d436-4dbc-9596-8fbbccfa2827 is in a terminal state: WorkflowFailedState
[2018-11-30 14:39:20,02] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2018-11-30 14:39:23,12] [info] Workflow polling stopped
[2018-11-30 14:39:23,13] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2018-11-30 14:39:23,14] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2018-11-30 14:39:23,14] [info] Aborting all running workflows.
[2018-11-30 14:39:23,14] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2018-11-30 14:39:23,20] [info] JobExecutionTokenDispenser stopped
[2018-11-30 14:39:23,20] [info] WorkflowStoreActor stopped
[2018-11-30 14:39:23,20] [info] WorkflowLogCopyRouter stopped
[2018-11-30 14:39:23,20] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2018-11-30 14:39:23,20] [info] WorkflowManagerActor All workflows finished
[2018-11-30 14:39:23,20] [info] Connection pools shut down
[2018-11-30 14:39:23,20] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2018-11-30 14:39:23,20] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2018-11-30 14:39:23,20] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2018-11-30 14:39:23,20] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2018-11-30 14:39:23,20] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2018-11-30 14:39:23,20] [info] WorkflowManagerActor stopped
[2018-11-30 14:39:23,20] [info] SubWorkflowStoreActor stopped
[2018-11-30 14:39:23,20] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2018-11-30 14:39:23,20] [info] DockerHashActor stopped
[2018-11-30 14:39:23,20] [info] IoProxy stopped
[2018-11-30 14:39:23,20] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2018-11-30 14:39:23,21] [info] JobStoreActor stopped
[2018-11-30 14:39:23,21] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2018-11-30 14:39:23,21] [info] KvWriteActor Shutting down: 0 queued messages to process
[2018-11-30 14:39:23,21] [info] CallCacheWriteActor stopped
[2018-11-30 14:39:23,21] [info] ServiceRegistryActor stopped
[2018-11-30 14:39:23,25] [info] Database closed
[2018-11-30 14:39:23,25] [info] Stream materializer shut down
Workflow 7a43f040-d436-4dbc-9596-8fbbccfa2827 transitioned to state Failed
[2018-11-30 14:39:23,29] [info] Automatic shutdown of the async connection
[2018-11-30 14:39:23,29] [info] Gracefully shutdown sentry threads.
[2018-11-30 14:39:23,29] [info] Shutdown finished.
(encode-atac-seq-pipeline) goldrath@Goldrath-vbox:~/Documents/ATACPipeline/atac-seq-pipeline$ exit
exit

Script done on 2018-11-30 15:30:11-0500