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WDL ERROR

Dear GATK Community,

I received following error during test run of WDL HaplotypeCaller:

2017-01-02 15:01:47,64] [error] WorkflowManagerActor Workflow a5ba5d7d-5c07-4929-a6e0-561c9e3c64c3 failed (during ExecutingWorkflowState): Call helloHaplotypeCaller.HaplotypeCaller:NA:1: return code was 1
java.lang.Exception: Call helloHaplotypeCaller.HaplotypeCaller:NA:1: return code was 1
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor$class.badReturnCodeResponse$lzycompute$1(SharedFileSystemAsyncJobExecutionActor.scala:334)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor$class.badReturnCodeResponse$1(SharedFileSystemAsyncJobExecutionActor.scala:333)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor$class.processReturnCode(SharedFileSystemAsyncJobExecutionActor.scala:364)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.processReturnCode(ConfigAsyncJobExecutionActor.scala:115)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor$class.poll(SharedFileSystemAsyncJobExecutionActor.scala:378)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.poll(ConfigAsyncJobExecutionActor.scala:115)
at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$cromwell$backend$async$AsyncBackendJobExecutionActor$$robustPoll$1.apply(AsyncBackendJobExecutionActor.scala:56)
at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$cromwell$backend$async$AsyncBackendJobExecutionActor$$robustPoll$1.apply(AsyncBackendJobExecutionActor.scala:56)
at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
at cromwell.backend.async.AsyncBackendJobExecutionActor$class.withRetry(AsyncBackendJobExecutionActor.scala:41)
at cromwell.backend.async.AsyncBackendJobExecutionActor$class.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustPoll(AsyncBackendJobExecutionActor.scala:56)
at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:70)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:171)
at akka.actor.Actor$class.aroundReceive(Actor.scala:484)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:115)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:526)
at akka.actor.ActorCell.invoke(ActorCell.scala:495)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
at akka.dispatch.Mailbox.run(Mailbox.scala:224)
at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

[2017-01-02 15:01:47,64] [info] WorkflowManagerActor WorkflowActor-a5ba5d7d-5c07-4929-a6e0-561c9e3c64c3 is in a terminal state: WorkflowFailedState
[2017-01-02 15:01:49,85] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
Workflow a5ba5d7d-5c07-4929-a6e0-561c9e3c64c3 transitioned to state Failed

I am following this link:

https://software.broadinstitute.org/wdl/userguide/topic?name=wdl-tutorials

Tagged:

Answers

  • The most important line is the first one

    2017-01-02 15:01:47,64] [error] WorkflowManagerActor Workflow a5ba5d7d-5c07-4929-a6e0-561c9e3c64c3 failed (during ExecutingWorkflowState): Call helloHaplotypeCaller.HaplotypeCaller:NA:1: return code was 1
    

    Which tells you that calling HaplotypeCaller failed (return code was 1). You will have to look in the cromwell-execution directory for that call to read the log files, to figure out what went wrong. The rest of the output is just the error propagating through cromwell untill it exits, so that gives you no information about what went wrong with HaplotypeCaller

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    @Redmar_van_den_Berg is correct! The error message serves to alert you to the simple fact that something went wrong. For more information on the error, you'll have to look in your stderr file, which you can find using the instructions in this article.

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