(encode-atac-seq-pipeline) [jtobias@node107 atac-seq-pipeline]$ java -jar -Dconfig.file=backends/backend.conf cromwell-34.jar run atac.wdl -i ${INPUT}
[2018-11-06 15:15:51,17] [info] Running with database db.url = jdbc:hsqldb:mem:4c814dd9-f69a-41e0-9a14-75e19ffe30b2;shutdown=false;hsqldb.tx=mvcc
[2018-11-06 15:16:02,63] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-11-06 15:16:02,64] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-11-06 15:16:02,75] [info] Running with database db.url = jdbc:hsqldb:mem:5cda0f73-247c-4c60-8030-2fa3e310e5bd;shutdown=false;hsqldb.tx=mvcc
[2018-11-06 15:16:03,10] [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
[2018-11-06 15:16:03,11] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-11-06 15:16:03,11] [info] Using noop to send events.
[2018-11-06 15:16:03,39] [info] Slf4jLogger started
[2018-11-06 15:16:03,60] [info] Workflow heartbeat configuration:
{
  "cromwellId" : "cromid-6143e90",
  "heartbeatInterval" : "2 minutes",
  "ttl" : "10 minutes",
  "writeBatchSize" : 10000,
  "writeThreshold" : 10000
}
[2018-11-06 15:16:03,64] [info] Metadata summary refreshing every 2 seconds.
[2018-11-06 15:16:03,72] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-11-06 15:16:03,72] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-11-06 15:16:03,72] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2018-11-06 15:16:04,50] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2018-11-06 15:16:04,52] [info] SingleWorkflowRunnerActor: Version 34
[2018-11-06 15:16:04,52] [info] JES batch polling interval is 33333 milliseconds
[2018-11-06 15:16:04,52] [info] JES batch polling interval is 33333 milliseconds
[2018-11-06 15:16:04,52] [info] JES batch polling interval is 33333 milliseconds
[2018-11-06 15:16:04,53] [info] PAPIQueryManager Running with 3 workers
[2018-11-06 15:16:04,53] [info] SingleWorkflowRunnerActor: Submitting workflow
[2018-11-06 15:16:04,58] [info] Unspecified type (Unspecified version) workflow 775c5649-e134-4c8e-a6ec-7cb6d211fffd submitted
[2018-11-06 15:16:04,63] [info] SingleWorkflowRunnerActor: Workflow submitted 775c5649-e134-4c8e-a6ec-7cb6d211fffd
[2018-11-06 15:16:04,63] [info] 1 new workflows fetched
[2018-11-06 15:16:04,63] [info] WorkflowManagerActor Starting workflow 775c5649-e134-4c8e-a6ec-7cb6d211fffd
[2018-11-06 15:16:04,64] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData
[2018-11-06 15:16:04,64] [info] WorkflowManagerActor Successfully started WorkflowActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd
[2018-11-06 15:16:04,64] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2018-11-06 15:16:04,65] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2018-11-06 15:16:04,71] [info] MaterializeWorkflowDescriptorActor [775c5649]: Parsing workflow as WDL draft-2
[2018-11-06 15:16:16,82] [info] MaterializeWorkflowDescriptorActor [775c5649]: Call-to-Backend assignments: atac.filter -> Local, atac.pool_ta -> Local, atac.reproducibility_overlap -> Local, atac.pool_ta_pr2 -> Local, atac.xcor -> Local, atac.spr -> Local, atac.overlap_pr -> Local, atac.macs2_pr1 -> Local, atac.bowtie2 -> Local, atac.ataqc -> Local, atac.macs2 -> Local, atac.macs2_ppr1 -> Local, atac.overlap -> Local, atac.bam2ta -> Local, atac.macs2_pr2 -> Local, atac.qc_report -> Local, atac.read_genome_tsv -> Local, atac.idr_pr -> Local, atac.trim_adapter -> Local, atac.reproducibility_idr -> Local, atac.pool_ta_pr1 -> Local, atac.idr -> Local, atac.idr_ppr -> Local, atac.macs2_ppr2 -> Local, atac.overlap_ppr -> Local, atac.macs2_pooled -> Local
[2018-11-06 15:16:16,92] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,93] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,93] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,94] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,95] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,95] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,95] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,95] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,95] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,95] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,95] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,95] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:16,95] [warn] Local [775c5649]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-06 15:16:19,20] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Starting atac.read_genome_tsv
[2018-11-06 15:16:19,20] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Condition met: 'enable_idr'. Running conditional section
[2018-11-06 15:16:19,20] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Condition met: '!disable_xcor'. Running conditional section
[2018-11-06 15:16:19,20] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Condition met: '!true_rep_only'. Running conditional section
[2018-11-06 15:16:19,20] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Condition met: 'enable_idr'. Running conditional section
[2018-11-06 15:16:19,20] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Condition met: '!align_only && !true_rep_only && enable_idr'. Running conditional section
[2018-11-06 15:16:19,21] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Condition met: '!align_only && !true_rep_only'. Running conditional section
[2018-11-06 15:16:19,62] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.read_genome_tsv:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 15:16:20,07] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.read_genome_tsv:NA:1]: cat /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-read_genome_tsv/inputs/-1159565645/hg38_local.tsv
[2018-11-06 15:16:20,12] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.read_genome_tsv:NA:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-read_genome_tsv/execution/script
[2018-11-06 15:16:23,33] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Starting atac.trim_adapter (2 shards)
[2018-11-06 15:16:23,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 15:16:23,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 15:16:23,57] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:1:1]: python $(which encode_trim_adapter.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-trim_adapter/shard-1/execution/write_tsv_7a6e2a2733f7b381e744dcbf0e21816a.tmp \
	--adapters /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/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
[2018-11-06 15:16:23,57] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:0:1]: python $(which encode_trim_adapter.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-trim_adapter/shard-0/execution/write_tsv_464e638d2da5252b42cb60fff994baae.tmp \
	--adapters /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/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
[2018-11-06 15:16:23,57] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:1:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-trim_adapter/shard-1/execution/script
[2018-11-06 15:16:23,58] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:0:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-trim_adapter/shard-0/execution/script
[2018-11-06 15:16:23,83] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:0:1]: job id: 27917
[2018-11-06 15:16:23,83] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.read_genome_tsv:NA:1]: job id: 27857
[2018-11-06 15:16:23,83] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:1:1]: job id: 27919
[2018-11-06 15:16:23,83] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.read_genome_tsv:NA:1]: Status change from - to Done
[2018-11-06 15:16:23,83] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:1:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 15:16:23,84] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 15:16:55,04] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 15:16:57,02] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Starting atac.bowtie2
[2018-11-06 15:16:57,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:0:1]: Unrecognized runtime attribute keys: preemptible, disks, cpu, time, memory
[2018-11-06 15:16:57,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:0:1]: python $(which encode_bowtie2.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bowtie2/shard-0/inputs/1015755504/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.tar \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bowtie2/shard-0/inputs/-208639647/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.fastq.gz /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bowtie2/shard-0/inputs/-208639647/merge_fastqs_R2_ENCFF248EJF.subsampled.400.trim.merged.fastq.gz \
	--paired-end \
	--multimapping 4 \
	 \
	--nth 4
[2018-11-06 15:16:57,56] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:0:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bowtie2/shard-0/execution/script
[2018-11-06 15:16:58,73] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:0:1]: job id: 28267
[2018-11-06 15:16:58,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 15:17:01,36] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.trim_adapter:1:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 15:17:03,14] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Starting atac.bowtie2
[2018-11-06 15:17:03,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:1:1]: Unrecognized runtime attribute keys: preemptible, disks, cpu, time, memory
[2018-11-06 15:17:03,77] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:1:1]: python $(which encode_bowtie2.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bowtie2/shard-1/inputs/1015755504/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.tar \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bowtie2/shard-1/inputs/-216399006/merge_fastqs_R1_ENCFF641SFZ.subsampled.400.trim.merged.fastq.gz /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bowtie2/shard-1/inputs/-216399006/merge_fastqs_R2_ENCFF031ARQ.subsampled.400.trim.merged.fastq.gz \
	--paired-end \
	--multimapping 4 \
	 \
	--nth 4
[2018-11-06 15:17:03,78] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:1:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bowtie2/shard-1/execution/script
[2018-11-06 15:17:08,73] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:1:1]: job id: 28368
[2018-11-06 15:17:08,73] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:1:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:24:40,24] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:1:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:28:00,88] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bowtie2:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:28:06,75] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Starting atac.filter (2 shards)
[2018-11-06 16:28:07,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:28:07,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:28:07,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:0:1]: python $(which encode_filter.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-filter/shard-0/inputs/752450728/ENCFF341MYG.subsampled.400.trim.merged.bam \
	--paired-end \
	--multimapping 4 \
	--dup-marker picard \
	--mapq-thresh 30 \
	 \
	--nth 2
# ugly part to deal with optional outputs with Google JES backend

touch null
[2018-11-06 16:28:07,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:1:1]: python $(which encode_filter.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-filter/shard-1/inputs/744691369/ENCFF641SFZ.subsampled.400.trim.merged.bam \
	--paired-end \
	--multimapping 4 \
	--dup-marker picard \
	--mapq-thresh 30 \
	 \
	--nth 2
# ugly part to deal with optional outputs with Google JES backend

touch null
[2018-11-06 16:28:07,60] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:1:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-filter/shard-1/execution/script
[2018-11-06 16:28:07,60] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:0:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-filter/shard-0/execution/script
[2018-11-06 16:28:08,73] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:1:1]: job id: 16499
[2018-11-06 16:28:08,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:0:1]: job id: 16508
[2018-11-06 16:28:08,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:28:08,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:1:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:29:25,96] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:29:33,17] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.filter:1:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:29:38,56] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Starting atac.bam2ta (2 shards)
[2018-11-06 16:29:39,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:29:39,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:29:39,53] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:0:1]: python $(which encode_bam2ta.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bam2ta/shard-0/inputs/621937410/ENCFF341MYG.subsampled.400.trim.merged.nodup.bam \
	--paired-end \
	 \
	--regex-grep-v-ta 'chrM' \
	--subsample 0 \
[2018-11-06 16:29:39,53] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:1:1]: python $(which encode_bam2ta.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bam2ta/shard-1/inputs/614178051/ENCFF641SFZ.subsampled.400.trim.merged.nodup.bam \
	--paired-end \
	 \
	--regex-grep-v-ta 'chrM' \
	--subsample 0 \
[2018-11-06 16:29:39,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:0:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bam2ta/shard-0/execution/script
[2018-11-06 16:29:39,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:1:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-bam2ta/shard-1/execution/script
[2018-11-06 16:29:43,73] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:0:1]: job id: 17213
[2018-11-06 16:29:43,73] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:1:1]: job id: 17201
[2018-11-06 16:29:43,73] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:29:43,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:1:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:29:55,29] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:30:01,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.bam2ta:1:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:30:05,08] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Condition met: 'length(tas_) > 1'. Running conditional section
[2018-11-06 16:30:05,08] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Condition met: '!true_rep_only && length(tas_) > 1'. Running conditional section
[2018-11-06 16:30:07,19] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Starting atac.spr (2 shards), atac.macs2 (2 shards), atac.pool_ta, atac.xcor (2 shards)
[2018-11-06 16:30:07,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:30:07,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:30:07,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:30:07,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:30:07,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.pool_ta:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:30:07,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:30:07,53] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:30:07,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:0:1]: python $(which encode_xcor.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-xcor/shard-0/inputs/831068956/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz \
	--paired-end \
	--subsample 25000000 \
	--speak=0 \
	--nth 2
[2018-11-06 16:30:07,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:1:1]: python $(which encode_spr.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-spr/shard-1/inputs/823309597/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz \
	--paired-end
[2018-11-06 16:30:07,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:0:1]: python $(which encode_spr.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-spr/shard-0/inputs/831068956/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz \
	--paired-end
[2018-11-06 16:30:07,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:1:1]: python $(which encode_macs2_atac.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2/shard-1/inputs/823309597/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz \
	--gensz hs \
	--chrsz /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2/shard-1/inputs/-1414731392/hg38.chrom.sizes \
	--cap-num-peak 300000 \
	--pval-thresh 0.01 \
	--smooth-win 73 \
	--make-signal \
	--blacklist /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2/shard-1/inputs/-1414731392/hg38.blacklist.bed.gz

# ugly part to deal with optional outputs with Google JES backend

touch null
[2018-11-06 16:30:07,55] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:1:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-spr/shard-1/execution/script
[2018-11-06 16:30:07,55] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.pool_ta:NA:1]: python $(which encode_pool_ta.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-pool_ta/inputs/831068956/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-pool_ta/inputs/823309597/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz
[2018-11-06 16:30:07,55] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:1:1]: python $(which encode_xcor.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-xcor/shard-1/inputs/823309597/ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz \
	--paired-end \
	--subsample 25000000 \
	--speak=0 \
	--nth 2
[2018-11-06 16:30:07,55] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:0:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-xcor/shard-0/execution/script
[2018-11-06 16:30:07,55] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:0:1]: python $(which encode_macs2_atac.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2/shard-0/inputs/831068956/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz \
	--gensz hs \
	--chrsz /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2/shard-0/inputs/-1414731392/hg38.chrom.sizes \
	--cap-num-peak 300000 \
	--pval-thresh 0.01 \
	--smooth-win 73 \
	--make-signal \
	--blacklist /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2/shard-0/inputs/-1414731392/hg38.blacklist.bed.gz

# ugly part to deal with optional outputs with Google JES backend

touch null
[2018-11-06 16:30:07,55] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:0:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-spr/shard-0/execution/script
[2018-11-06 16:30:07,55] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.pool_ta:NA:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-pool_ta/execution/script
[2018-11-06 16:30:07,55] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:1:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-xcor/shard-1/execution/script
[2018-11-06 16:30:07,56] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:1:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2/shard-1/execution/script
[2018-11-06 16:30:07,57] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:0:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2/shard-0/execution/script
[2018-11-06 16:30:08,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:0:1]: job id: 17574
[2018-11-06 16:30:08,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.pool_ta:NA:1]: job id: 17573
[2018-11-06 16:30:08,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:1:1]: job id: 17583
[2018-11-06 16:30:08,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:0:1]: job id: 17641
[2018-11-06 16:30:08,75] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:1:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:30:08,78] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:30:08,83] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:30:08,86] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:1:1]: job id: 17627
[2018-11-06 16:30:08,86] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:1:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:30:08,96] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:0:1]: job id: 17619
[2018-11-06 16:30:08,99] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.pool_ta:NA:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:30:08,99] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:1:1]: job id: 17600
[2018-11-06 16:30:08,99] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:1:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:30:09,02] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:30:10,23] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.pool_ta:NA:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:30:10,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:30:11,27] [info] WorkflowExecutionActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd [775c5649]: Starting atac.macs2_pooled
[2018-11-06 16:30:11,52] [warn] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2_pooled:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-06 16:30:11,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2_pooled:NA:1]: python $(which encode_macs2_atac.py) \
	/home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2_pooled/inputs/1546065147/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.pooled.tagAlign.gz \
	--gensz hs \
	--chrsz /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2_pooled/inputs/-1414731392/hg38.chrom.sizes \
	--cap-num-peak 300000 \
	--pval-thresh 0.01 \
	--smooth-win 73 \
	--make-signal \
	--blacklist /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2_pooled/inputs/-1414731392/hg38.blacklist.bed.gz

# ugly part to deal with optional outputs with Google JES backend

touch null
[2018-11-06 16:30:11,56] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2_pooled:NA:1]: executing: /bin/bash /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-macs2_pooled/execution/script
[2018-11-06 16:30:12,13] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:1:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:30:12,54] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.xcor:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:30:12,57] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.spr:1:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:30:13,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2_pooled:NA:1]: job id: 18064
[2018-11-06 16:30:13,74] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2_pooled:NA:1]: Status change from - to WaitingForReturnCodeFile
[2018-11-06 16:32:01,10] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:32:39,77] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2:1:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:33:47,20] [info] BackgroundConfigAsyncJobExecutionActor [775c5649atac.macs2_pooled:NA:1]: Status change from WaitingForReturnCodeFile to Done
[2018-11-06 16:33:47,68] [error] WorkflowManagerActor Workflow 775c5649-e134-4c8e-a6ec-7cb6d211fffd failed (during ExecutingWorkflowState): 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: /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-xcor/shard-0/execution/stderr.
 Traceback (most recent call last):
  File "/home/jtobias/software/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 226, in run_shell_cmd
    p.returncode, cmd)
subprocess.CalledProcessError: Command 'Rscript --max-ppsize=500000 $(which run_spp.R) -rf -c=ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.25.0M.tagAlign.gz -p=2 -filtchr=chrM -savp=ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.25.0M.cc.plot.pdf -out=ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.25.0M.cc.qc -speak=0' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jtobias/software/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 102, in <module>
    main()
  File "/home/jtobias/software/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 91, in main
    ta_subsampled, args.speak, args.nth, args.out_dir)
  File "/home/jtobias/software/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 53, in xcor
    run_shell_cmd(cmd1)
  File "/home/jtobias/software/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 235, in run_shell_cmd
    raise Exception('Exception caught. Killed PID={}, PGID={}'.format(pid,pgid))
Exception: Exception caught. Killed PID=17928, PGID=17928

cromwell.backend.standard.StandardAsyncExecutionActor$$anon$2: Failed to evaluate job outputs:
Bad output 'macs2.bfilt_npeak': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2.bfilt_npeak_bb': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2.sig_pval': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2.sig_fc': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2.frip_qc': 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)

cromwell.backend.standard.StandardAsyncExecutionActor$$anon$2: Failed to evaluate job outputs:
Bad output 'macs2.bfilt_npeak': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2.bfilt_npeak_bb': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2.sig_pval': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2.sig_fc': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2.frip_qc': 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)

cromwell.backend.standard.StandardAsyncExecutionActor$$anon$2: Failed to evaluate job outputs:
Bad output 'macs2_pooled.bfilt_npeak': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2_pooled.bfilt_npeak_bb': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2_pooled.sig_pval': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2_pooled.sig_fc': Failed to find index Success(WomInteger(0)) on array:

Success([])

0
Bad output 'macs2_pooled.frip_qc': 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)

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: /home/jtobias/software/atac-seq-pipeline/cromwell-executions/atac/775c5649-e134-4c8e-a6ec-7cb6d211fffd/call-xcor/shard-1/execution/stderr.
 Traceback (most recent call last):
  File "/home/jtobias/software/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 226, in run_shell_cmd
    p.returncode, cmd)
subprocess.CalledProcessError: Command 'Rscript --max-ppsize=500000 $(which run_spp.R) -rf -c=ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.25.0M.tagAlign.gz -p=2 -filtchr=chrM -savp=ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.25.0M.cc.plot.pdf -out=ENCFF641SFZ.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.25.0M.cc.qc -speak=0' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jtobias/software/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 102, in <module>
    main()
  File "/home/jtobias/software/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 91, in main
    ta_subsampled, args.speak, args.nth, args.out_dir)
  File "/home/jtobias/software/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_xcor.py", line 53, in xcor
    run_shell_cmd(cmd1)
  File "/home/jtobias/software/miniconda3/envs/encode-atac-seq-pipeline/bin/encode_common.py", line 235, in run_shell_cmd
    raise Exception('Exception caught. Killed PID={}, PGID={}'.format(pid,pgid))
Exception: Exception caught. Killed PID=17912, PGID=17912

[2018-11-06 16:33:47,68] [info] WorkflowManagerActor WorkflowActor-775c5649-e134-4c8e-a6ec-7cb6d211fffd is in a terminal state: WorkflowFailedState
[2018-11-06 16:34:21,23] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2018-11-06 16:34:23,73] [info] Workflow polling stopped
[2018-11-06 16:34:23,81] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2018-11-06 16:34:23,81] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2018-11-06 16:34:23,85] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2018-11-06 16:34:23,85] [info] JobExecutionTokenDispenser stopped
[2018-11-06 16:34:23,85] [info] Aborting all running workflows.
[2018-11-06 16:34:23,85] [info] WorkflowStoreActor stopped
[2018-11-06 16:34:23,86] [info] WorkflowLogCopyRouter stopped
[2018-11-06 16:34:23,86] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2018-11-06 16:34:23,86] [info] WorkflowManagerActor All workflows finished
[2018-11-06 16:34:23,86] [info] WorkflowManagerActor stopped
[2018-11-06 16:34:23,86] [info] Connection pools shut down
[2018-11-06 16:34:23,86] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2018-11-06 16:34:23,86] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2018-11-06 16:34:23,86] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2018-11-06 16:34:23,86] [info] SubWorkflowStoreActor stopped
[2018-11-06 16:34:23,86] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2018-11-06 16:34:23,86] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2018-11-06 16:34:23,86] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2018-11-06 16:34:23,87] [info] KvWriteActor Shutting down: 0 queued messages to process
[2018-11-06 16:34:23,87] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2018-11-06 16:34:23,87] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2018-11-06 16:34:23,87] [info] CallCacheWriteActor stopped
[2018-11-06 16:34:23,87] [info] IoProxy stopped
[2018-11-06 16:34:23,87] [info] DockerHashActor stopped
[2018-11-06 16:34:23,91] [info] JobStoreActor stopped
[2018-11-06 16:34:23,91] [info] ServiceRegistryActor stopped
[2018-11-06 16:34:23,92] [info] Database closed
[2018-11-06 16:34:23,92] [info] Stream materializer shut down
Workflow 775c5649-e134-4c8e-a6ec-7cb6d211fffd transitioned to state Failed
[2018-11-06 16:34:23,97] [info] Automatic shutdown of the async connection
[2018-11-06 16:34:23,97] [info] Gracefully shutdown sentry threads.
[2018-11-06 16:34:23,97] [info] Shutdown finished.