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Failed to find index Success(WomInteger(0)) #15

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chengwsh opened this issue Jul 10, 2018 · 14 comments
Closed

Failed to find index Success(WomInteger(0)) #15

chengwsh opened this issue Jul 10, 2018 · 14 comments

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@chengwsh
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2018-07-08 17:12:05,62] [info] Running with database db.url = jdbc:hsqldb:mem:b928854f-1b26-4f74-8a45-e72f73b30968;shutdown=false;hsqldb.tx=mvcc
[2018-07-08 17:12:11,01] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-07-08 17:12:11,02] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-07-08 17:12:11,10] [info] Running with database db.url = jdbc:hsqldb:mem:b55a6427-b864-4e72-9858-1211b6533178;shutdown=false;hsqldb.tx=mvcc
[2018-07-08 17:12:11,42] [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
[2018-07-08 17:12:11,42] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-07-08 17:12:11,43] [info] Using noop to send events.
[2018-07-08 17:12:11,69] [info] Slf4jLogger started
[2018-07-08 17:12:11,87] [info] Workflow heartbeat configuration:
{
"cromwellId" : "cromid-df3d320",
"heartbeatInterval" : "2 minutes",
"ttl" : "10 minutes",
"writeBatchSize" : 10000,
"writeThreshold" : 10000
}
[2018-07-08 17:12:11,91] [info] Metadata summary refreshing every 2 seconds.
[2018-07-08 17:12:11,95] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2018-07-08 17:12:11,95] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-07-08 17:12:11,95] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-07-08 17:12:12,71] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2018-07-08 17:12:12,73] [info] JES batch polling interval is 33333 milliseconds
[2018-07-08 17:12:12,73] [info] JES batch polling interval is 33333 milliseconds
[2018-07-08 17:12:12,73] [info] JES batch polling interval is 33333 milliseconds
[2018-07-08 17:12:12,73] [info] PAPIQueryManager Running with 3 workers
[2018-07-08 17:12:12,74] [info] SingleWorkflowRunnerActor: Submitting workflow
[2018-07-08 17:12:12,78] [info] Unspecified type (Unspecified version) workflow 068f45d8-f29a-4335-8c0e-a711391af811 submitted
[2018-07-08 17:12:12,83] [info] SingleWorkflowRunnerActor: Workflow submitted 068f45d8-f29a-4335-8c0e-a711391af811
[2018-07-08 17:12:12,83] [info] 1 new workflows fetched
[2018-07-08 17:12:12,83] [info] WorkflowManagerActor Starting workflow 068f45d8-f29a-4335-8c0e-a711391af811
[2018-07-08 17:12:12,84] [info] WorkflowManagerActor Successfully started WorkflowActor-068f45d8-f29a-4335-8c0e-a711391af811
[2018-07-08 17:12:12,84] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2018-07-08 17:12:12,84] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData
[2018-07-08 17:12:12,85] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2018-07-08 17:12:12,89] [info] MaterializeWorkflowDescriptorActor [068f45d8]: Parsing workflow as WDL draft-2
[2018-07-08 17:13:26,22] [info] MaterializeWorkflowDescriptorActor [068f45d8]: Call-to-Backend assignments: chip.macs2 -> Local, chip.bam2ta_ctl -> Local, chip.spp_ppr2 -> Local, chip.bwa -> Local, chip .qc_report -> Local, chip.bwa_ctl -> Local, chip.filter -> Local, chip.overlap -> Local, chip.pool_ta -> Local, chip.idr_ppr -> Local, chip.filter_ctl -> Local, chip.macs2_pr2 -> Local, chip.spp_pr1 -> Local, chip.read_genome_tsv -> Local, chip.merge_fastq_ctl -> Local, chip.macs2_ppr1 -> Local, chip.pool_ta_pr2 -> Local, chip.trim_fastq -> Local, chip.overlap_ppr -> Local, chip.bam2ta -> Local, chip. pool_ta_ctl -> Local, chip.reproducibility_idr -> Local, chip.spp_pooled -> Local, chip.fraglen_mean -> Local, chip.spr -> Local, chip.bam2ta_no_filt -> Local, chip.macs2_pr1 -> Local, chip.fingerprint -> Local, chip.xcor -> Local, chip.spp_pr2 -> Local, chip.spp -> Local, chip.merge_fastq -> Local, chip.bam2ta_no_filt_R1 -> Local, chip.reproducibility_overlap -> Local, chip.overlap_pr -> Local, chip. idr -> Local, chip.macs2_ppr2 -> Local, chip.bwa_R1 -> Local, chip.spp_ppr1 -> Local, chip.macs2_pooled -> Local, chip.idr_pr -> Local, chip.choose_ctl -> Local, chip.pool_ta_pr1 -> Local
[2018-07-08 17:13:26,34] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,35] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,36] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:26,37] [warn] Local [068f45d8]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-07-08 17:13:28,66] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Starting chip.read_genome_tsv
[2018-07-08 17:13:28,67] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Condition met: '!align_only && !true_rep_only'. Running conditional section
[2018-07-08 17:13:28,68] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Condition met: '!true_rep_only'. Running conditional section
[2018-07-08 17:13:28,87] [warn] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.read_genome_tsv:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-07-08 17:13:29,34] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.read_genome_tsv:NA:1]: echo "Reading genome_tsv /home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068 f45d8-f29a-4335-8c0e-a711391af811/call-read_genome_tsv/inputs/1532045310/mm10.tsv ..."
[2018-07-08 17:13:29,46] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.read_genome_tsv:NA:1]: executing: /bin/bash /home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d 8-f29a-4335-8c0e-a711391af811/call-read_genome_tsv/execution/script
[2018-07-08 17:13:29,70] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Condition NOT met: 'peak_caller_ == "macs2"'. Bypassing conditional section
[2018-07-08 17:13:29,70] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Condition met: 'enable_idr'. Running conditional section
[2018-07-08 17:13:29,70] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Condition met: 'enable_idr'. Running conditional section
[2018-07-08 17:13:29,70] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Condition met: 'peak_caller_ == "spp"'. Running conditional section
[2018-07-08 17:13:29,70] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Condition met: 'peak_caller_ == "spp"'. Running conditional section
[2018-07-08 17:13:29,71] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Condition met: '!align_only && !true_rep_only && enable_idr'. Running conditional section
[2018-07-08 17:13:31,99] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.read_genome_tsv:NA:1]: job id: 18903
[2018-07-08 17:13:32,00] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.read_genome_tsv:NA:1]: Status change from - to Done
[2018-07-08 17:13:32,80] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Starting chip.merge_fastq_ctl, chip.merge_fastq
[2018-07-08 17:13:33,74] [warn] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.merge_fastq_ctl:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-07-08 17:13:33,74] [warn] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.merge_fastq:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-07-08 17:13:33,85] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.merge_fastq_ctl:0:1]: python $(which encode_merge_fastq.py)
/home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-4335-8c0e-a711391af811/call-merge_fastq_ctl/shard-0/execution/write_tsv_609523603b8830d2bf2d45a4a71d8dd7.tmp

--nth 2
[2018-07-08 17:13:33,85] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.merge_fastq:0:1]: python $(which encode_merge_fastq.py)
/home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-4335-8c0e-a711391af811/call-merge_fastq/shard-0/execution/write_tsv_577d047f7bb8a8ea8c6ee89ee3d97c7b.tmp

--nth 2
[2018-07-08 17:13:33,85] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.merge_fastq:0:1]: executing: /bin/bash /home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29 a-4335-8c0e-a711391af811/call-merge_fastq/shard-0/execution/script
[2018-07-08 17:13:33,85] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.merge_fastq_ctl:0:1]: executing: /bin/bash /home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8 -f29a-4335-8c0e-a711391af811/call-merge_fastq_ctl/shard-0/execution/script
[2018-07-08 17:13:36,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.merge_fastq:0:1]: job id: 18944
[2018-07-08 17:13:36,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.merge_fastq_ctl:0:1]: job id: 18946
[2018-07-08 17:13:36,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.merge_fastq:0:1]: Status change from - to Done
[2018-07-08 17:13:36,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.merge_fastq_ctl:0:1]: Status change from - to Done
[2018-07-08 17:13:38,92] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Starting chip.bwa, chip.bwa_ctl
[2018-07-08 17:13:39,74] [warn] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa:0:1]: Unrecognized runtime attribute keys: preemptible, disks, cpu, time, memory
[2018-07-08 17:13:39,74] [warn] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa_ctl:0:1]: Unrecognized runtime attribute keys: preemptible, disks, cpu, time, memory
[2018-07-08 17:13:39,76] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa:0:1]: python $(which encode_bwa.py)
/home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-4335-8c0e-a711391af811/call-bwa/shard-0/inputs/1424220334/mm10_no_alt_analysis_set_ENCODE.fasta.tar
/home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-4335-8c0e-a711391af811/call-bwa/shard-0/inputs/-1993312639/merge_fastqs_R1_RYBP.merged.fastq.gz

--nth 4
[2018-07-08 17:13:39,76] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa_ctl:0:1]: python $(which encode_bwa.py)
/home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-4335-8c0e-a711391af811/call-bwa_ctl/shard-0/inputs/1424220334/mm10_no_alt_analysis_set_ENCODE.fasta.tar
/home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-4335-8c0e-a711391af811/call-bwa_ctl/shard-0/inputs/1654728541/merge_fastqs_R1_IgG.merged.fastq.gz

--nth 4
[2018-07-08 17:13:39,77] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa_ctl:0:1]: executing: /bin/bash /home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-43 35-8c0e-a711391af811/call-bwa_ctl/shard-0/execution/script
[2018-07-08 17:13:39,77] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa:0:1]: executing: /bin/bash /home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-4335-8 c0e-a711391af811/call-bwa/shard-0/execution/script
[2018-07-08 17:13:41,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa_ctl:0:1]: job id: 19040
[2018-07-08 17:13:41,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa:0:1]: job id: 19041
[2018-07-08 17:13:41,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa_ctl:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-07-08 17:13:41,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-07-08 18:03:30,01] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa_ctl:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-07-08 18:03:35,69] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Starting chip.filter_ctl
[2018-07-08 18:03:35,73] [warn] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter_ctl:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-07-08 18:03:35,77] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter_ctl:0:1]: python $(which encode_filter.py)
/home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-4335-8c0e-a711391af811/call-filter_ctl/shard-0/inputs/1613485654/IgG.merged.bam


--dup-marker picard
--mapq-thresh 30
\

ugly part to deal with optional outputs with Google JES backend

touch null
[2018-07-08 18:03:35,88] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter_ctl:0:1]: executing: /bin/bash /home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a -4335-8c0e-a711391af811/call-filter_ctl/shard-0/execution/script
[2018-07-08 18:03:36,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter_ctl:0:1]: job id: 1170
[2018-07-08 18:03:36,99] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter_ctl:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-07-08 18:07:57,26] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bwa:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-07-08 18:08:02,93] [info] WorkflowExecutionActor-068f45d8-f29a-4335-8c0e-a711391af811 [068f45d8]: Starting chip.bam2ta_no_filt, chip.filter
[2018-07-08 18:08:03,73] [warn] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bam2ta_no_filt:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-07-08 18:08:03,73] [warn] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-07-08 18:08:03,74] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bam2ta_no_filt:0:1]: python $(which encode_bam2ta.py)
/home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-4335-8c0e-a711391af811/call-bam2ta_no_filt/shard-0/inputs/600163450/RYBP.merged.bam

--disable-tn5-shift
--regex-grep-v-ta 'chrM'
--subsample 0
[2018-07-08 18:08:03,74] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bam2ta_no_filt:0:1]: executing: /bin/bash /home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8- f29a-4335-8c0e-a711391af811/call-bam2ta_no_filt/shard-0/execution/script
[2018-07-08 18:08:03,76] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter:0:1]: python $(which encode_filter.py)
/home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-4335-8c0e-a711391af811/call-filter/shard-0/inputs/600163450/RYBP.merged.bam


--dup-marker picard
--mapq-thresh 30
\

ugly part to deal with optional outputs with Google JES backend

touch null
[2018-07-08 18:08:03,77] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter:0:1]: executing: /bin/bash /home/chengwsh/Encode/chip-seq-pipeline2/cromwell-executions/chip/068f45d8-f29a-433 5-8c0e-a711391af811/call-filter/shard-0/execution/script
[2018-07-08 18:08:06,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bam2ta_no_filt:0:1]: job id: 2502
[2018-07-08 18:08:06,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter:0:1]: job id: 2516
[2018-07-08 18:08:06,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bam2ta_no_filt:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-07-08 18:08:06,97] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter:0:1]: Status change from - to WaitingForReturnCodeFile
[2018-07-08 18:10:26,92] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.bam2ta_no_filt:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-07-08 18:11:32,77] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter_ctl:0: 1]: Status change from WaitingForReturnCodeFile to Done
[2018-07-08 18:16:25,24] [info] BackgroundConfigAsyncJobExecutionActor [068f45d8chip.filter:0:1]: Status change from WaitingForReturnCodeFile to Done
[2018-07-08 18:16:26,14] [error] WorkflowManagerActor Workflow 068f45d8-f29a-4335-8c0e-a711391af81 1 failed (during ExecutingWorkflowState): Failed to evaluate job outputs:
Bad output 'filter_ctl.nodup_bai': Failed to find index Success(WomInteger(0)) on array:

Success([])

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

Success([])

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

Success([])

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

Success([])

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

Success([])

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

Success([])

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

Success([])

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

Success([])

0
at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$handleExecutionSuccess$1 (StandardAsyncExecutionActor.scala:786)
at scala.util.Success.$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(ForkJoinExecutorConfig urator.scala:43)
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)

Failed to evaluate job outputs:
Bad output 'filter.nodup_bai': Failed to find index Success(WomInteger(0)) on array:

Success([])

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

Success([])

0
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
at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$handleExecutionSuccess$1 (StandardAsyncExecutionActor.scala:786)
at scala.util.Success.$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(ForkJoinExecutorConfig urator.scala:43)
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)

[2018-07-08 18:16:26,14] [info] WorkflowManagerActor WorkflowActor-068f45d8-f29a-4335-8c0e-a711391 af811 is in a terminal state: WorkflowFailedState
[2018-07-08 18:17:28,68] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2018-07-08 18:17:31,99] [info] Workflow polling stopped
[2018-07-08 18:17:32,12] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2018-07-08 18:17:32,12] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2018-07-08 18:17:32,15] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2018-07-08 18:17:32,17] [info] Aborting all running workflows.
[2018-07-08 18:17:32,19] [info] JobExecutionTokenDispenser stopped
[2018-07-08 18:17:32,19] [info] WorkflowStoreActor stopped
[2018-07-08 18:17:32,24] [info] WorkflowLogCopyRouter stopped
[2018-07-08 18:17:32,24] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2018-07-08 18:17:32,24] [info] WorkflowManagerActor stopped
[2018-07-08 18:17:32,24] [info] WorkflowManagerActor All workflows finished
[2018-07-08 18:17:32,24] [info] Connection pools shut down
[2018-07-08 18:17:32,24] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2018-07-08 18:17:32,24] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2018-07-08 18:17:32,24] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2018-07-08 18:17:32,24] [info] SubWorkflowStoreActor stopped
[2018-07-08 18:17:32,24] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2018-07-08 18:17:32,24] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2018-07-08 18:17:32,24] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2018-07-08 18:17:32,27] [info] DockerHashActor stopped
[2018-07-08 18:17:32,27] [info] IoProxy stopped
[2018-07-08 18:17:32,30] [info] KvWriteActor Shutting down: 0 queued messages to process
[2018-07-08 18:17:32,30] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2018-07-08 18:17:32,30] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2018-07-08 18:17:32,30] [info] CallCacheWriteActor stopped
[2018-07-08 18:17:32,33] [info] JobStoreActor stopped
[2018-07-08 18:17:32,34] [info] ServiceRegistryActor stopped
[2018-07-08 18:17:32,36] [info] Database closed
[2018-07-08 18:17:32,36] [info] Stream materializer shut down
Workflow 068f45d8-f29a-4335-8c0e-a711391af811 transitioned to state Failed
[2018-07-08 18:17:32,46] [info] Automatic shutdown of the async connection
[2018-07-08 18:17:32,46] [info] Gracefully shutdown sentry threads.
[2018-07-08 18:17:32,46] [info] Shutdown finished.
@leepc12
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leepc12 commented Jul 10, 2018 •
edited
Loading

Please run the following on the working directory where you ran the pipeline and post debug.tar here. This will make

find . -type f \
-name 'stdout' -or \
-name 'stderr' -or \
-name 'script' -or \
-name '*.qc' -or \
-name '*.txt' -or \
-name '*.log \
| xargs tar -cvf debug.tar

@chengwsh
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debug (2).zip
Thank you.

@leepc12
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leepc12 commented Jul 11, 2018

Please check if you have picard.jar in your $PATH after activating Conda environment.

$ source activate encode-chip-seq-pipeline
$ which picard.jar
$ which samtools
$ echo $PATH

@kirstyjamieson
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Hi Jin, I am also getting this error with the test data.

-bash-4.1$ export PATH="/netapp/home/kirsty.jamieson/miniconda3/bin:$PATH"
-bash-4.1$ source activate encode-chip-seq-pipeline
(encode-chip-seq-pipeline) -bash-4.1$ which picard.jar
~/miniconda3/envs/encode-chip-seq-pipeline/bin/picard.jar
(encode-chip-seq-pipeline) -bash-4.1$ which samtools
~/miniconda3/envs/encode-chip-seq-pipeline/bin/samtools
(encode-chip-seq-pipeline) -bash-4.1$ echo $PATH
/netapp/home/kirsty.jamieson/miniconda3/envs/encode-chip-seq-pipeline/bin:/netapp/home/kirsty.jamieson/miniconda3/bin:/usr/local/sge/bin/linux-x64:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/netopt/bin

examples/local/ENCSR936XTK_subsampled.json

{
    "chip.pipeline_type" : "tf",
    "chip.genome_tsv" : "test_genome_database/hg38_local.tsv",
    "chip.fastqs" : [
        [["test_sample/ENCSR936XTK/fastq_subsampled/rep1-R1.subsampled.67.fastq.gz",
          "test_sample/ENCSR936XTK/fastq_subsampled/rep1-R2.subsampled.67.fastq.gz"]],
        [["test_sample/ENCSR936XTK/fastq_subsampled/rep2-R1.subsampled.67.fastq.gz",
          "test_sample/ENCSR936XTK/fastq_subsampled/rep2-R2.subsampled.67.fastq.gz"]]
    ],
    "chip.ctl_fastqs" : [
        [["test_sample/ENCSR936XTK/fastq_subsampled/ctl1-R1.subsampled.80.fastq.gz",
          "test_sample/ENCSR936XTK/fastq_subsampled/ctl1-R2.subsampled.80.fastq.gz"]],
        [["test_sample/ENCSR936XTK/fastq_subsampled/ctl2-R1.subsampled.80.fastq.gz",
          "test_sample/ENCSR936XTK/fastq_subsampled/ctl2-R2.subsampled.80.fastq.gz"]]
    ],

    "chip.paired_end" : true,

    "chip.always_use_pooled_ctl" : true,
    "chip.title" : "ENCSR936XTK (subsampled 1/67)",
    "chip.description" : "ZNF143 ChIP-seq on human GM12878"
}

test.sh.txt
test.sh.o522226.txt
debug_[#15_KJ_12_5_18].tar.gz

@leepc12
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leepc12 commented Dec 5, 2018

Error:

PID=52604: [Tue Dec 04 15:05:13 PST 2018] picard.sam.markduplicates.MarkDuplicates INPUT=[rep1-R1.subsampled.67.merged.filt.bam] OUTPUT=rep1-R1.subsampled.67.merged.dupmark.bam METRICS_FILE=rep1-R1.subsampled.67.merged.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
PID=52604: [Tue Dec 04 15:05:13 PST 2018] Executing as kirsty.jamieson@id69 on Linux 2.6.32-696.30.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Picard version: 2.10.6-SNAPSHOT
PID=52604: INFO 2018-12-04 15:05:14     MarkDuplicates  Start of doWork freeMemory: 22135416; totalMemory: 28311552; maxMemory: 4294967296
PID=52604: INFO 2018-12-04 15:05:14     MarkDuplicates  Reading input file and constructing read end information.
PID=52604: INFO 2018-12-04 15:05:14     MarkDuplicates  Will retain up to 15561475 data points before spilling to disk.
PID=52604: INFO 2018-12-04 15:05:22     MarkDuplicates  Read 909380 records. 0 pairs never matched.
PID=52604: INFO 2018-12-04 15:05:22     MarkDuplicates  After buildSortedReadEndLists freeMemory: 580621504; totalMemory: 811597824; maxMemory: 4294967296
PID=52604: INFO 2018-12-04 15:05:22     MarkDuplicates  Will retain up to 134217728 duplicate indices before spilling to disk.
PID=52604: INFO 2018-12-04 15:05:22     MarkDuplicates  Traversing read pair information and detecting duplicates.
PID=52604: INFO 2018-12-04 15:05:22     MarkDuplicates  Traversing fragment information and detecting duplicates.
PID=52604: INFO 2018-12-04 15:05:22     MarkDuplicates  Sorting list of duplicate records.
PID=52604: INFO 2018-12-04 15:05:22     MarkDuplicates  After generateDuplicateIndexes freeMemory: 804662104; totalMemory: 1886388224; maxMemory: 4294967296
PID=52604: INFO 2018-12-04 15:05:22     MarkDuplicates  Marking 1850 records as duplicates.
PID=52604: INFO 2018-12-04 15:05:22     MarkDuplicates  Found 3 optical duplicate clusters.
PID=52604: INFO 2018-12-04 15:05:22     MarkDuplicates  Reads are assumed to be ordered by: coordinate
PID=52604: #
PID=52604: # A fatal error has been detected by the Java Runtime Environment:
PID=52604: #
PID=52604: #  SIGSEGV (0xb) at pc=0x00002b3fc6568344, pid=52604, tid=52666
PID=52604: #
PID=52604: # JRE version: OpenJDK Runtime Environment (11.0.1+13) (build 11.0.1+13-LTS)
PID=52604: # Java VM: OpenJDK 64-Bit Server VM (11.0.1+13-LTS, mixed mode, tiered, compressed oops, g1 gc, linux-amd64)
PID=52604: # Problematic frame:
PID=52604: # V  [libjvm.so+0x7f8344]  G1ParScanThreadState::copy_to_survivor_space(InCSetState, oopDesc*, markOopDesc*)+0x334
PID=52604: #
PID=52604: # Core dump will be written. Default location: /scrapp/kirsty.jamieson/chip-seq-pipeline2/cromwell-executions/chip/27f31472-68b7-48aa-a66f-0f8e98299750/call-filter/shard-0/execution/core.52604
PID=52604: #
PID=52604: # An error report file with more information is saved as:
PID=52604: # /scrapp/kirsty.jamieson/chip-seq-pipeline2/cromwell-executions/chip/27f31472-68b7-48aa-a66f-0f8e98299750/call-filter/shard-0/execution/hs_err_pid52604.log
PID=52604: #
PID=52604: # If you would like to submit a bug report, please visit:
PID=52604: #   http://www.azulsystems.com/support/
PID=52604: #

This should be fixed in v1.1.3. f8f2e88

Please git pull to update the pipeline and try again.

@kirstyjamieson
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I updated the pipeline and got the same error, so I reinstalled the pipeline again. I get a new error this time

Uncaught error from thread [cromwell-system-akka.dispatchers.backend-dispatcher-62]: cromwell/backend/async/FailedNonRetryableExecutionHandle, shutting down JVM since 'akka.jvm-exit-on-fatal-error' is enabled for ActorSystem[cromwell-system]

debug_[#15_KJ_12_7_18].tar.gz
test.sh.o527395.txt
test.sh.txt

@leepc12
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leepc12 commented Dec 7, 2018

Did you download genome database correctly on test_genome_database/? One of the files in it is missing.

gzip: /scrapp/kirsty.jamieson/chip-seq-pipeline2/cromwell-executions/chip/56c459cc-49af-4b86-8425-5a5423b2377d/call-spp/shard-1/inputs/1911427029/hg38.blacklist.bed.gz: No such file or directory

@kirstyjamieson
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I did, but now I am noticing that cromwell-34.jar, test_sample/ and test_genome_database/ have all disappeared after this failed run.

@leepc12
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leepc12 commented Dec 7, 2018

You mean those files and directories on /scrapp/kirsty.jamieson/chip-seq-pipeline2?

@kirstyjamieson
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Yes

@leepc12
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leepc12 commented Dec 7, 2018

It's weird. Pipeline does not delete any file on a working directory. Do you have any disk limit/quota on your pipeline git directory. $HOME usually has limited quota on HPC. I think you need to contact with your system admin. Or run it on a scratch directory.

@kirstyjamieson
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scrapp/ is a scratch directory with no individual user limits, 511 GB available. I had this issue early on with the atac-seq-pipeline ENCODE-DCC/atac-seq-pipeline#55 (comment).

I was also wondering where you found this error:
gzip: /scrapp/kirsty.jamieson/chip-seq-pipeline2/cromwell-executions/chip/56c459cc-49af-4b86-8425-5a5423b2377d/call-spp/shard-1/inputs/1911427029/hg38.blacklist.bed.gz: No such file or directory because I didn't see it in cromwell-workflow-logs/

@leepc12
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leepc12 commented Dec 10, 2018

Log files are on cromwell-executions/chip/ not on cromwell-workflow-logs/. I found it in the following log file:

./cromwell-executions/chip/2793a6b9-72d7-4e23-832a-e7619955e11a/call-spp_pr1/shard-1/execution/stderr

Is the entire directory (test_sample/ and test_genome_database/) missing after running a pipeline?
Does your cluster's file system /scrapp/ allow hard-linking of files?
I think you need to figure out the disk problem first. Pipeline cannot work without data on test_sample/ and test_genome_database/.

@leepc12
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leepc12 commented Sep 9, 2019

Closing this due to long inactivity

@leepc12 leepc12 closed this as completed Sep 9, 2019
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@leepc12 @kirstyjamieson @chengwsh