Cromwell on Cluster

shair_rosenbergshair_rosenberg L'Institut du Cerveau et de la Moelle Épinière (ICM) Salpetriere Hospital, Paris , FranceMember
edited October 2016 in Ask the WDL team

Hi,

I tried to run WDL pipeline for Mutect2. I run it on a cluster. I understood that running Cromwell on cluster is more complicated but I did not find instructions how to do it (not in userguide and not in the excecution part).

Anyway - I tried to run and received the following error:

[2016-10-19 23:10:10,52] [info] SharedFileSystemAsyncJobExecutionActor [b0d0dbe4MuTect2_workflow.MuTect2_task:NA:1]: executing: /bin/bash /cs/icore/shair/program_files/wdl/cromwell-executions/MuTect2_workflow/b0d0dbe4-2d08-467f-9c61-e07961130ae8/call-MuTect2_task/execution/script
[2016-10-19 23:10:10,52] [info] SharedFileSystemAsyncJobExecutionActor [b0d0dbe4MuTect2_workflow.MuTect2_task:NA:1]: command: "/bin/bash" "/cs/icore/shair/program_files/wdl/cromwell-executions/MuTect2_workflow/b0d0dbe4-2d08-467f-9c61-e07961130ae8/call-MuTect2_task/execution/script.submit"
[2016-10-19 23:10:10,53] [info] SharedFileSystemAsyncJobExecutionActor [b0d0dbe4MuTect2_workflow.MuTect2_task:NA:1]: job id: 3543
[2016-10-19 23:10:13,60] [error] WorkflowManagerActor Workflow b0d0dbe4-2d08-467f-9c61-e07961130ae8 failed (during ExecutingWorkflowState): java.lang.Exception: Call MuTect2_workflow.MuTect2_task: return code was 1
[2016-10-19 23:10:13,60] [info] WorkflowManagerActor WorkflowActor-b0d0dbe4-2d08-467f-9c61-e07961130ae8 is in a terminal state: WorkflowFailedState
[2016-10-19 23:10:17,02] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2016-10-19 23:10:17,03] [error] Workflow b0d0dbe4-2d08-467f-9c61-e07961130ae8 transitioned to state Failed
java.lang.RuntimeException: Workflow b0d0dbe4-2d08-467f-9c61-e07961130ae8 transitioned to state Failed
        at cromwell.engine.workflow.SingleWorkflowRunnerActor$RunnerData.addFailure(SingleWorkflowRunnerActor.scala:53)
        at cromwell.engine.workflow.SingleWorkflowRunnerActor$$anonfun$2.applyOrElse(SingleWorkflowRunnerActor.scala:132)
        at cromwell.engine.workflow.SingleWorkflowRunnerActor$$anonfun$2.applyOrElse(SingleWorkflowRunnerActor.scala:110)
        at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
        at akka.actor.FSM$class.processEvent(FSM.scala:663)
        at cromwell.engine.workflow.SingleWorkflowRunnerActor.akka$actor$LoggingFSM$$super$processEvent(SingleWorkflowRunnerActor.scala:70)
        at akka.actor.LoggingFSM$class.processEvent(FSM.scala:799)
        at cromwell.engine.workflow.SingleWorkflowRunnerActor.processEvent(SingleWorkflowRunnerActor.scala:70)
        at akka.actor.FSM$class.akka$actor$FSM$$processMsg(FSM.scala:657)
        at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:651)
        at akka.actor.Actor$class.aroundReceive(Actor.scala:484)
        at cromwell.server.CromwellRootActor.aroundReceive(CromwellRootActor.scala:27)
        at akka.actor.ActorCell.receiveMessage(ActorCell.scala:526)
        at akka.actor.ActorCell.invoke(ActorCell.scala:495)
        at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
        at akka.dispatch.Mailbox.run(Mailbox.scala:224)
        at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
        at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
        at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
        at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
        at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Workflow b0d0dbe4-2d08-467f-9c61-e07961130ae8 transitioned to state Failed
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  • shair_rosenbergshair_rosenberg L'Institut du Cerveau et de la Moelle Épinière (ICM) Salpetriere Hospital, Paris , FranceMember

    Thanks! Now it runs well. I will look for the ticket you mentioned.

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