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| [2018-12-22 19:38:42,36] [info] Running with database db.url = jdbc:hsqldb:mem:64cb552b-816c-4f93-bafd-21743b589b42;shutdown=false;hsqldb.tx=mvcc | |
| [2018-12-22 19:38:55,72] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000 | |
| [2018-12-22 19:38:55,83] [info] [RenameWorkflowOptionsInMetadata] 100% | |
| [2018-12-22 19:38:56,42] [info] Running with database db.url = jdbc:hsqldb:mem:f9eb9b02-87e7-4e76-883b-2aaced01ab36;shutdown=false;hsqldb.tx=mvcc | |
| [2018-12-22 19:38:57,18] [info] Slf4jLogger started | |
| [2018-12-22 19:38:57,65] [info] Workflow heartbeat configuration: | |
| { | |
| "cromwellId" : "cromid-1478c70", | |
| "heartbeatInterval" : "2 minutes", | |
| "ttl" : "10 minutes", | |
| "writeBatchSize" : 10000, | |
| "writeThreshold" : 10000 | |
| } | |
| [2018-12-22 19:38:57,72] [info] Metadata summary refreshing every 2 seconds. | |
| [2018-12-22 19:38:57,92] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. | |
| [2018-12-22 19:38:57,92] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. | |
| [2018-12-22 19:38:58,01] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. | |
| [2018-12-22 19:38:59,71] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. | |
| [2018-12-22 19:38:59,81] [info] SingleWorkflowRunnerActor: Version 36 | |
| [2018-12-22 19:38:59,82] [info] SingleWorkflowRunnerActor: Submitting workflow | |
| [2018-12-22 19:39:00,03] [info] Unspecified type (Unspecified version) workflow 5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29 submitted | |
| [2018-12-22 19:39:00,04] [info] SingleWorkflowRunnerActor: Workflow submitted [38;5;2m5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29[0m | |
| [2018-12-22 19:39:00,11] [info] 1 new workflows fetched | |
| [2018-12-22 19:39:00,11] [info] WorkflowManagerActor Starting workflow [38;5;2m5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29[0m | |
| [2018-12-22 19:39:00,12] [info] WorkflowManagerActor Successfully started WorkflowActor-5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29 | |
| [2018-12-22 19:39:00,12] [info] Retrieved 1 workflows from the WorkflowStoreActor | |
| [2018-12-22 19:39:00,12] [[38;5;220mwarn[0m] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData | |
| [2018-12-22 19:39:00,13] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. | |
| [2018-12-22 19:39:00,43] [info] MaterializeWorkflowDescriptorActor [[38;5;2m5abd010a[0m]: Parsing workflow as CWL v1.0 | |
| [2018-12-22 19:39:00,72] [info] Pre-Processing /tmp/cwl_temp_dir_12896957636850987565/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl | |
| WARNING: An illegal reflective access operation has occurred | |
| WARNING: Illegal reflective access by org.python.core.PySystemState (file:/root/reproducible-workflows/CWL/SingleStepWorkflow/cromwell-36.jar) to method java.io.Console.encoding() | |
| WARNING: Please consider reporting this to the maintainers of org.python.core.PySystemState | |
| WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations | |
| WARNING: All illegal access operations will be denied in a future release | |
| [2018-12-22 19:39:43,66] [info] Pre-Processing /tmp/cwl_temp_dir_12896957636850987565/bwa-pe.cwl | |
| [2018-12-22 19:39:44,50] [info] MaterializeWorkflowDescriptorActor [[38;5;2m5abd010a[0m]: Call-to-Backend assignments: bwa -> Local | |
| [2018-12-22 19:39:46,93] [info] WorkflowExecutionActor-5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29 [[38;5;2m5abd010a[0m]: Starting bwa | |
| [2018-12-22 19:39:48,94] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m5abd010a[0mbwa:NA:1]: [38;5;5m'bwa' 'mem' '-M' '-R' '@RG\tID:A\tSM:A\tPL:Illumina' '/cromwell-executions/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl/5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29/call-bwa/inputs/-534407894/Homo_sapiens_assembly38.fasta' '/cromwell-executions/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl/5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29/call-bwa/inputs/-534407894/CM-M40-O40-K20-R1_R1.fastq.gz' '/cromwell-executions/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl/5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29/call-bwa/inputs/-534407894/CM-M40-O40-K20-R1_R2.fastq.gz' '-t' '8'[0m | |
| [2018-12-22 19:39:49,11] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m5abd010a[0mbwa:NA:1]: executing: # make sure there is no preexisting Docker CID file | |
| rm -f /root/reproducible-workflows/CWL/SingleStepWorkflow/cromwell-executions/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl/5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29/call-bwa/execution/docker_cid | |
| # run as in the original configuration without --rm flag (will remove later) | |
| docker run \ | |
| --cidfile /root/reproducible-workflows/CWL/SingleStepWorkflow/cromwell-executions/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl/5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29/call-bwa/execution/docker_cid \ | |
| -i \ | |
| \ | |
| --entrypoint /bin/bash \ | |
| -v /root/reproducible-workflows/CWL/SingleStepWorkflow/cromwell-executions/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl/5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29/call-bwa:/cromwell-executions/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl/5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29/call-bwa \ | |
| genomicpariscentre/bwa@sha256:d59552f71821d0be66bb0cb8325b3b04e58f98601ee93b5a926c1960b544ccc9 /cromwell-executions/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl/5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29/call-bwa/execution/script | |
| # get the return code (working even if the container was detached) | |
| rc=$(docker wait [38;5;5mcat /root/reproducible-workflows/CWL/SingleStepWorkflow/cromwell-executions/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl/5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29/call-bwa/execution/docker_cid[0m) | |
| # remove the container after waiting | |
| docker rm [38;5;5mcat /root/reproducible-workflows/CWL/SingleStepWorkflow/cromwell-executions/cwl_temp_file_5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29.cwl/5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29/call-bwa/execution/docker_cid[0m | |
| # return exit code | |
| exit $rc | |
| [2018-12-22 19:39:52,95] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m5abd010a[0mbwa:NA:1]: job id: 14670 | |
| [2018-12-22 19:39:52,96] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m5abd010a[0mbwa:NA:1]: Status change from - to WaitingForReturnCode | |
| [2018-12-22 19:40:09,70] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m5abd010a[0mbwa:NA:1]: Status change from WaitingForReturnCode to Done | |
| [2018-12-22 19:40:10,58] [[38;5;1merror[0m] WorkflowManagerActor Workflow 5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29 failed (during ExecutingWorkflowState): java.lang.Exception: The job was aborted from outside Cromwell | |
| at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:247) | |
| at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:184) | |
| at scala.PartialFunction$OrElse.apply(PartialFunction.scala:168) | |
| at akka.actor.FSM.processEvent(FSM.scala:687) | |
| at akka.actor.FSM.processEvent$(FSM.scala:681) | |
| at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowExecutionActor.scala:49) | |
| at akka.actor.LoggingFSM.processEvent(FSM.scala:820) | |
| at akka.actor.LoggingFSM.processEvent$(FSM.scala:802) | |
| at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.processEvent(WorkflowExecutionActor.scala:49) | |
| at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:678) | |
| at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:672) | |
| at akka.actor.Actor.aroundReceive(Actor.scala:517) | |
| at akka.actor.Actor.aroundReceive$(Actor.scala:515) | |
| at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$Timers$$super$aroundReceive(WorkflowExecutionActor.scala:49) | |
| at akka.actor.Timers.aroundReceive(Timers.scala:55) | |
| at akka.actor.Timers.aroundReceive$(Timers.scala:40) | |
| at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.aroundReceive(WorkflowExecutionActor.scala:49) | |
| 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) | |
| [2018-12-22 19:40:10,59] [info] WorkflowManagerActor WorkflowActor-5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29 is in a terminal state: WorkflowFailedState | |
| [2018-12-22 19:40:17,92] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'. | |
| [2018-12-22 19:40:17,94] [info] Workflow polling stopped | |
| [2018-12-22 19:40:17,95] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds | |
| [2018-12-22 19:40:17,95] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds | |
| [2018-12-22 19:40:17,95] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds | |
| [2018-12-22 19:40:17,95] [info] Aborting all running workflows. | |
| [2018-12-22 19:40:17,95] [info] JobExecutionTokenDispenser stopped | |
| [2018-12-22 19:40:17,95] [info] WorkflowStoreActor stopped | |
| [2018-12-22 19:40:17,96] [info] WorkflowLogCopyRouter stopped | |
| [2018-12-22 19:40:17,96] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds | |
| [2018-12-22 19:40:17,96] [info] WorkflowManagerActor All workflows finished | |
| [2018-12-22 19:40:17,96] [info] WorkflowManagerActor stopped | |
| [2018-12-22 19:40:17,96] [info] Connection pools shut down | |
| [2018-12-22 19:40:17,96] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds | |
| [2018-12-22 19:40:17,96] [info] Shutting down JobStoreActor - Timeout = 1800 seconds | |
| [2018-12-22 19:40:17,96] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds | |
| [2018-12-22 19:40:17,96] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds | |
| [2018-12-22 19:40:17,96] [info] SubWorkflowStoreActor stopped | |
| [2018-12-22 19:40:17,96] [info] Shutting down DockerHashActor - Timeout = 1800 seconds | |
| [2018-12-22 19:40:17,96] [info] CallCacheWriteActor Shutting down: 0 queued messages to process | |
| [2018-12-22 19:40:17,96] [info] Shutting down IoProxy - Timeout = 1800 seconds | |
| [2018-12-22 19:40:17,96] [info] JobStoreActor stopped | |
| [2018-12-22 19:40:17,96] [info] CallCacheWriteActor stopped | |
| [2018-12-22 19:40:17,96] [info] KvWriteActor Shutting down: 0 queued messages to process | |
| [2018-12-22 19:40:17,96] [info] WriteMetadataActor Shutting down: 0 queued messages to process | |
| [2018-12-22 19:40:17,96] [info] DockerHashActor stopped | |
| [2018-12-22 19:40:17,96] [info] IoProxy stopped | |
| [2018-12-22 19:40:17,96] [info] ServiceRegistryActor stopped | |
| [2018-12-22 19:40:17,98] [info] Database closed | |
| [2018-12-22 19:40:17,98] [info] Stream materializer shut down | |
| [2018-12-22 19:40:18,01] [info] WDL HTTP import resolver closed | |
| Workflow 5abd010a-8fa0-4d1b-8d2a-9b591ebc5c29 transitioned to state Failed |
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