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September 21, 2018 20:16
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| ```sbatch --mem=8g --partition=broadwl run_atac.sh``` | |
| ``` | |
| [2018-09-21 20:02:15,33] [info] Running with database db.url = jdbc:hsqldb:mem:d3447b12-159a-4e42-84ed-95008b9b4607;shutdown=false;hsqldb.tx=mvcc | |
| [2018-09-21 20:02:35,30] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000 | |
| [2018-09-21 20:02:35,33] [info] [RenameWorkflowOptionsInMetadata] 100% | |
| [2018-09-21 20:02:35,80] [info] Running with database db.url = jdbc:hsqldb:mem:f9c12bea-bc1b-4b04-9c39-4a44d4e12b5b;shutdown=false;hsqldb.tx=mvcc | |
| [2018-09-21 20:02:36,59] [ESC[38;5;220mwarnESC[0m] This actor factory is deprecated. Please use cromwell.backend.google.pipelines.v1alpha2.PipelinesApiLifecycleActorFactory for PAPI v1 or cromwell.backend.google.pipelines.v2alpha1.Pipel$nesApiLifecycleActorFactory for PAPI v2 | |
| [2018-09-21 20:02:36,65] [ESC[38;5;220mwarnESC[0m] Couldn't find a suitable DSN, defaulting to a Noop one. | |
| [2018-09-21 20:02:36,66] [info] Using noop to send events. | |
| [2018-09-21 20:02:37,03] [info] Slf4jLogger started | |
| [2018-09-21 20:02:37,33] [info] Workflow heartbeat configuration: | |
| { | |
| "cromwellId" : "cromid-6252614", | |
| "heartbeatInterval" : "2 minutes", | |
| "ttl" : "10 minutes", | |
| "writeBatchSize" : 10000, | |
| "writeThreshold" : 10000 | |
| } | |
| [2018-09-21 20:02:37,57] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. | |
| [2018-09-21 20:02:37,61] [info] Metadata summary refreshing every 2 seconds. | |
| [2018-09-21 20:02:37,77] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. | |
| [2018-09-21 20:02:37,81] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. | |
| [2018-09-21 20:02:40,83] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. | |
| [2018-09-21 20:02:40,93] [info] SingleWorkflowRunnerActor: Version 34 | |
| [2018-09-21 20:02:40,96] [info] SingleWorkflowRunnerActor: Submitting workflow | |
| [2018-09-21 20:02:40,98] [info] JES batch polling interval is 33333 milliseconds | |
| [2018-09-21 20:02:40,99] [info] JES batch polling interval is 33333 milliseconds | |
| [2018-09-21 20:02:41,01] [info] JES batch polling interval is 33333 milliseconds | |
| [2018-09-21 20:02:41,05] [info] PAPIQueryManager Running with 3 workers | |
| [2018-09-21 20:02:41,07] [info] Unspecified type (Unspecified version) workflow bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec submitted | |
| [2018-09-21 20:02:41,35] [info] SingleWorkflowRunnerActor: Workflow submitted ESC[38;5;2mbb6365e3-f3d7-4fb6-a5ac-7bb61a55bfecESC[0m | |
| [2018-09-21 20:02:41,37] [ESC[38;5;220mwarnESC[0m] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData | |
| [2018-09-21 20:02:41,41] [info] 1 new workflows fetched | |
| [2018-09-21 20:02:41,41] [info] WorkflowManagerActor Starting workflow ESC[38;5;2mbb6365e3-f3d7-4fb6-a5ac-7bb61a55bfecESC[0m | |
| [2018-09-21 20:02:41,41] [info] WorkflowManagerActor Successfully started WorkflowActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec | |
| [2018-09-21 20:02:41,41] [info] Retrieved 1 workflows from the WorkflowStoreActor | |
| [2018-09-21 20:02:41,43] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. | |
| [2018-09-21 20:02:42,12] [info] MaterializeWorkflowDescriptorActor [ESC[38;5;2mbb6365e3ESC[0m]: Parsing workflow as WDL draft-2 | |
| [2018-09-21 20:03:04,60] [info] MaterializeWorkflowDescriptorActor [ESC[38;5;2mbb6365e3ESC[0m]: Call-to-Backend assignments: atac.bam2ta -> slurm, atac.idr -> slurm, atac.read_genome_tsv -> slurm, atac.trim_adapter -> slurm, atac.macs2_p | |
| ooled -> slurm, atac.overlap -> slurm, atac.ataqc -> slurm, atac.pool_ta_pr1 -> slurm, atac.macs2 -> slurm, atac.bowtie2 -> slurm, atac.spr -> slurm, atac.qc_report -> slurm, atac.overlap_pr -> slurm, atac.macs2_pr1 -> slurm, atac.pool_t | |
| a -> slurm, atac.macs2_ppr1 -> slurm, atac.macs2_pr2 -> slurm, atac.xcor -> slurm, atac.reproducibility_idr -> slurm, atac.filter -> slurm, atac.idr_pr -> slurm, atac.pool_ta_pr2 -> slurm, atac.macs2_ppr2 -> slurm, atac.idr_ppr -> slurm, | |
| atac.overlap_ppr -> slurm, atac.reproducibility_overlap -> slurm | |
| [2018-09-21 20:03:05,10] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,16] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,16] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,17] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,21] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,24] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,25] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,26] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,26] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,27] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [preemptible, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,27] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,27] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,27] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,28] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,29] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,29] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,29] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,29] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:05,29] [ESC[38;5;220mwarnESC[0m] slurm [ESC[38;5;2mbb6365e3ESC[0m]: Key/s [disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. | |
| [2018-09-21 20:03:07,66] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Starting atac.read_genome_tsv | |
| [2018-09-21 20:03:07,66] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: '!align_only && !true_rep_only && enable_idr'. Running conditional section | |
| [2018-09-21 20:03:07,67] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: '!true_rep_only'. Running conditional section | |
| [2018-09-21 20:03:07,70] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: 'enable_idr'. Running conditional section | |
| [2018-09-21 20:03:07,70] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: '!disable_xcor'. Running conditional section | |
| [2018-09-21 20:03:07,70] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: '!align_only && !true_rep_only'. Running conditional section | |
| [2018-09-21 20:03:07,71] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Condition met: 'enable_idr'. Running conditional section | |
| [2018-09-21 20:03:08,06] [ESC[38;5;220mwarnESC[0m] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: Unrecognized runtime attribute keys: disks | |
| [2018-09-21 20:03:09,55] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: ESC[38;5;5mcat /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-read_genome_tsv/inputs/378634365/hg19.tsvESC[0m | |
| [2018-09-21 20:03:09,61] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: executing: sbatch \ | |
| --export=ALL \ | |
| -J cromwell_bb6365e3_read_genome_tsv \ | |
| -D /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-read_genome_tsv \ | |
| -o /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-read_genome_tsv/execution/stdout \ | |
| -e /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-read_genome_tsv/execution/stderr \ | |
| -t 60 \ | |
| -n 1 \ | |
| --ntasks-per-node=1 \ | |
| --cpus-per-task=1 \ | |
| --mem=4000 \ | |
| -p broadwl \ | |
| \ | |
| --wrap "/bin/bash /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-read_genome_tsv/execution/script" | |
| [2018-09-21 20:03:12,42] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Starting atac.trim_adapter (2 shards) | |
| [2018-09-21 20:03:12,63] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: job id: 49925419 | |
| [2018-09-21 20:03:12,65] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-09-21 20:03:12,90] [ESC[38;5;220mwarnESC[0m] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: Unrecognized runtime attribute keys: disks | |
| [2018-09-21 20:03:12,92] [ESC[38;5;220mwarnESC[0m] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: Unrecognized runtime attribute keys: disks | |
| [2018-09-21 20:03:13,33] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: ESC[38;5;5mpython $(which encode_trim_adapter.py) \ | |
| /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0/execution/write_tsv_3274ebda6c46dc57a250f066328e4929.tmp \ | |
| --adapters /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0/execution/write_tsv_d41d8cd98f00b204e9800998ecf8427e.tmp \ | |
| --paired-end \ | |
| --auto-detect-adapter \ | |
| --min-trim-len 5 \ | |
| --err-rate 0.1 \ | |
| --nth 1ESC[0m | |
| [2018-09-21 20:03:13,36] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: ESC[38;5;5mpython $(which encode_trim_adapter.py) \ | |
| /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1/execution/write_tsv_4ec997f74112c76af08be107c84bd1f0.tmp \ | |
| --adapters /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1/execution/write_tsv_d41d8cd98f00b204e9800998ecf8427e.tmp \ | |
| --paired-end \ | |
| --auto-detect-adapter \ | |
| --min-trim-len 5 \ | |
| --err-rate 0.1 \ | |
| --nth 1ESC[0m | |
| [2018-09-21 20:03:13,41] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: executing: sbatch \ | |
| --export=ALL \ | |
| -J cromwell_bb6365e3_trim_adapter \ | |
| -D /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0 \ | |
| -o /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0/execution/stdout \ | |
| -e /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0/execution/stderr \ | |
| -t 1440 \ | |
| -n 1 \ | |
| --ntasks-per-node=1 \ | |
| --cpus-per-task=1 \ | |
| --mem=12000 \ | |
| -p broadwl \ | |
| \ | |
| --wrap "/bin/bash /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-0/execution/script" | |
| [2018-09-21 20:03:13,47] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: executing: sbatch \ | |
| --export=ALL \ | |
| -J cromwell_bb6365e3_trim_adapter \ | |
| -D /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1 \ | |
| -o /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1/execution/stdout \ | |
| -e /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1/execution/stderr \ | |
| -t 1440 \ | |
| -n 1 \ | |
| --ntasks-per-node=1 \ | |
| --cpus-per-task=1 \ | |
| --mem=12000 \ | |
| -p broadwl \ | |
| \ | |
| --wrap "/bin/bash /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-trim_adapter/shard-1/execution/script" | |
| [2018-09-21 20:03:17,62] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: job id: 49925421 | |
| [2018-09-21 20:03:17,64] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: job id: 49925422 | |
| [2018-09-21 20:03:17,64] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-09-21 20:03:17,66] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: Status change from - to WaitingForReturnCodeFile | |
| [2018-09-21 20:04:24,26] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.read_genome_tsv:NA:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-09-21 20:05:48,94] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:0:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-09-21 20:05:50,22] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Starting atac.bowtie2 | |
| [2018-09-21 20:05:50,85] [ESC[38;5;220mwarnESC[0m] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:0:1]: Unrecognized runtime attribute keys: preemptible, disks | |
| [2018-09-21 20:05:50,87] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.trim_adapter:1:1]: Status change from WaitingForReturnCodeFile to Done | |
| [2018-09-21 20:05:50,91] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:0:1]: ESC[38;5;5mpython $(which encode_bowtie2.py) \ | |
| /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/inputs/646531885/male.hg19.fa.tar \ | |
| /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/inputs/-1650399814/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.fastq.gz /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/inputs/-1650399814/merge_fastqs_R2_ENCFF248EJF.subsampled.400.trim.merged.fastq.gz \ | |
| --paired-end \ | |
| --multimapping 4 \ | |
| \ | |
| --nth 2ESC[0m | |
| [2018-09-21 20:05:51,79] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:0:1]: executing: sbatch \ | |
| --export=ALL \ | |
| -J cromwell_bb6365e3_bowtie2 \ | |
| -D /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0 \ | |
| -o /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/execution/stdout \ | |
| -e /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/execution/stderr \ | |
| -t 2880 \ | |
| -n 1 \ | |
| --ntasks-per-node=1 \ | |
| --cpus-per-task=2 \ | |
| --mem=16000 \ | |
| -p broadwl \ | |
| \ | |
| --wrap "/bin/bash /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/execution/script" | |
| [2018-09-21 20:05:52,27] [info] WorkflowExecutionActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec [ESC[38;5;2mbb6365e3ESC[0m]: Starting atac.bowtie2 | |
| [2018-09-21 20:05:52,90] [ESC[38;5;220mwarnESC[0m] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:1:1]: Unrecognized runtime attribute keys: preemptible, disks | |
| [2018-09-21 20:05:53,00] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:1:1]: ESC[38;5;5mpython $(which encode_bowtie2.py) \ | |
| /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/inputs/646531885/male.hg19.fa.tar \ | |
| /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/inputs/-1658159173/merge_fastqs_R1_ENCFF641SFZ.subsampled.400.trim.merged.fastq.gz /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/inputs/-1658159173/merge_fastqs_R2_ENCFF031ARQ.subsampled.400.trim.merged.fastq.gz \ | |
| --paired-end \ | |
| --multimapping 4 \ | |
| \ | |
| --nth 2ESC[0m | |
| [2018-09-21 20:05:53,08] [info] DispatchedConfigAsyncJobExecutionActor [ESC[38;5;2mbb6365e3ESC[0matac.bowtie2:1:1]: executing: sbatch \ | |
| --export=ALL \ | |
| -J cromwell_bb6365e3_bowtie2 \ | |
| -D /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1 \ | |
| -o /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/execution/stdout \ | |
| -e /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/execution/stderr \ | |
| -t 2880 \ | |
| -n 1 \ | |
| --ntasks-per-node=1 \ | |
| --cpus-per-task=2 \ | |
| --mem=16000 \ | |
| -p broadwl \ | |
| \ | |
| --wrap "/bin/bash /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/execution/script" | |
| [2018-09-21 20:05:55,36] [ESC[38;5;1merrorESC[0m] WorkflowManagerActor Workflow bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec failed (during ExecutingWorkflowState): java.lang.RuntimeException: Unable to start job. Check the stderr file for possi | |
| ble errors: /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-0/execution/stderr.submit | |
| at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.$anonfun$execute$2(SharedFileSystemAsyncJobExecutionActor.scala:131) | |
| at scala.util.Either.fold(Either.scala:188) | |
| at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:126) | |
| at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121) | |
| at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:208) | |
| at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600) | |
| at scala.util.Try$.apply(Try.scala:209) | |
| at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600) | |
| at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600) | |
| at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:208) | |
| at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915) | |
| at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907) | |
| at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:208) | |
| at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65) | |
| at cromwell.core.retry.Retry$.withRetry(Retry.scala:37) | |
| at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:61) | |
| at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:65) | |
| at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:88) | |
| at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172) | |
| at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172) | |
| at akka.actor.Actor.aroundReceive(Actor.scala:517) | |
| at akka.actor.Actor.aroundReceive$(Actor.scala:515) | |
| at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:208) | |
| at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588) | |
| at akka.actor.ActorCell.invoke(ActorCell.scala:557) | |
| at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258) | |
| at akka.dispatch.Mailbox.run(Mailbox.scala:225) | |
| at akka.dispatch.Mailbox.exec(Mailbox.scala:235) | |
| at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) | |
| at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) | |
| at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) | |
| at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) | |
| java.lang.RuntimeException: Unable to start job. Check the stderr file for possible errors: /project2/name1/name2/ASP/atac-seq-pipeline/cromwell-executions/atac/bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec/call-bowtie2/shard-1/execution/stderr.submit | |
| at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.$anonfun$execute$2(SharedFileSystemAsyncJobExecutionActor.scala:131) | |
| at scala.util.Either.fold(Either.scala:188) | |
| at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:126) | |
| at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121) | |
| at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:208) | |
| at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600) | |
| at scala.util.Try$.apply(Try.scala:209) | |
| at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600) | |
| at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600) | |
| at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:208) | |
| at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915) | |
| at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907) | |
| at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:208) | |
| at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65) | |
| at cromwell.core.retry.Retry$.withRetry(Retry.scala:37) | |
| at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:61) | |
| at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:65) | |
| at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:88) | |
| at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172) | |
| at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172) | |
| at akka.actor.Actor.aroundReceive(Actor.scala:517) | |
| at akka.actor.Actor.aroundReceive$(Actor.scala:515) | |
| at cromwell.backend.impl.sfs.config.DispatchedConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:208) | |
| at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588) | |
| at akka.actor.ActorCell.invoke(ActorCell.scala:557) | |
| at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258) | |
| at akka.dispatch.Mailbox.run(Mailbox.scala:225) | |
| at akka.dispatch.Mailbox.exec(Mailbox.scala:235) | |
| 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) | |
| [2018-09-21 20:05:55,37] [info] WorkflowManagerActor WorkflowActor-bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec is in a terminal state: WorkflowFailedState | |
| [2018-09-21 20:06:04,87] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'. | |
| [2018-09-21 20:06:07,83] [info] Workflow polling stopped | |
| [2018-09-21 20:06:07,84] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds | |
| [2018-09-21 20:06:07,85] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds | |
| [2018-09-21 20:06:07,87] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds | |
| [2018-09-21 20:06:07,88] [info] JobExecutionTokenDispenser stopped | |
| [2018-09-21 20:06:07,89] [info] WorkflowStoreActor stopped | |
| [2018-09-21 20:06:07,88] [info] Aborting all running workflows. | |
| [2018-09-21 20:06:07,90] [info] WorkflowLogCopyRouter stopped | |
| [2018-09-21 20:06:07,90] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds | |
| [2018-09-21 20:06:07,90] [info] WorkflowManagerActor All workflows finished | |
| [2018-09-21 20:06:07,91] [info] WorkflowManagerActor stopped | |
| [2018-09-21 20:06:07,91] [info] Connection pools shut down | |
| [2018-09-21 20:06:07,91] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds | |
| [2018-09-21 20:06:07,91] [info] Shutting down JobStoreActor - Timeout = 1800 seconds | |
| [2018-09-21 20:06:07,91] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds | |
| [2018-09-21 20:06:07,91] [info] CallCacheWriteActor Shutting down: 0 queued messages to process | |
| [2018-09-21 20:06:07,91] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds | |
| [2018-09-21 20:06:07,91] [info] Shutting down DockerHashActor - Timeout = 1800 seconds | |
| [2018-09-21 20:06:07,91] [info] Shutting down IoProxy - Timeout = 1800 seconds | |
| [2018-09-21 20:06:07,91] [info] SubWorkflowStoreActor stopped | |
| [2018-09-21 20:06:07,91] [info] JobStoreActor stopped | |
| [2018-09-21 20:06:07,91] [info] CallCacheWriteActor stopped | |
| [2018-09-21 20:06:07,91] [info] DockerHashActor stopped | |
| [2018-09-21 20:06:07,91] [info] IoProxy stopped | |
| [2018-09-21 20:06:07,92] [info] WriteMetadataActor Shutting down: 0 queued messages to process | |
| [2018-09-21 20:06:07,92] [info] KvWriteActor Shutting down: 0 queued messages to process | |
| [2018-09-21 20:06:07,92] [info] ServiceRegistryActor stopped | |
| [2018-09-21 20:06:07,96] [info] Database closed | |
| [2018-09-21 20:06:07,96] [info] Stream materializer shut down | |
| Workflow bb6365e3-f3d7-4fb6-a5ac-7bb61a55bfec transitioned to state Failed | |
| [2018-09-21 20:06:08,05] [info] Automatic shutdown of the async connection | |
| [2018-09-21 20:06:08,05] [info] Gracefully shutdown sentry threads. | |
| [2018-09-21 20:06:08,07] [info] Shutdown finished. | |
| ``` |
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