LATEST RELEASE: May 23, 2018
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Service notice: The "QueuedInCromwell" issue is resolved. All workflows should now be running normally. If you experience further issues of this type, please report them here.

[ERROR] the local copy message must have path set.

Hi Firecloud Team,

I submitted a workflow to FC yesterday. But, just one of the tasks was failed. I tried three times and got the same ERROR message as following in workflow.log. And, there is no log files for the failed task. I have no idea how to fix it. Thank you very much!

2017-11-06 22:48:09,085 ERROR - JesAsyncBackendJobExecutionActor [UUID(34df5fa6)CNVSomaticPairWorkflow.ModelSegmentsNormal:NA:1]: Error attempting to Execute
cromwell.backend.impl.jes.statuspolling.JesApiQueryManager$JesApiException: Unable to complete JES Api Request
    at cromwell.backend.impl.jes.statuspolling.RunCreation$$anon$1.onFailure(RunCreation.scala:24)
    at com.google.api.client.googleapis.batch.json.JsonBatchCallback.onFailure(JsonBatchCallback.java:54)
    at com.google.api.client.googleapis.batch.json.JsonBatchCallback.onFailure(JsonBatchCallback.java:50)
    at com.google.api.client.googleapis.batch.BatchUnparsedResponse.parseAndCallback(BatchUnparsedResponse.java:223)
    at com.google.api.client.googleapis.batch.BatchUnparsedResponse.parseNextResponse(BatchUnparsedResponse.java:155)
    at com.google.api.client.googleapis.batch.BatchRequest.execute(BatchRequest.java:253)
    at cromwell.backend.impl.jes.statuspolling.JesPollingActor.runBatch(JesPollingActor.scala:63)
    at cromwell.backend.impl.jes.statuspolling.JesPollingActor.cromwell$backend$impl$jes$statuspolling$JesPollingActor$$handleBatch(JesPollingActor.scala:57)
    at cromwell.backend.impl.jes.statuspolling.JesPollingActor$$anonfun$receive$1.applyOrElse(JesPollingActor.scala:36)
    at akka.actor.Actor$class.aroundReceive(Actor.scala:496)
    at cromwell.backend.impl.jes.statuspolling.JesPollingActor.aroundReceive(JesPollingActor.scala:22)
    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$WorkQueue.runTask(ForkJoinPool.java:1339)
    at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
    at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: cromwell.backend.impl.jes.statuspolling.JesApiQueryManager$GoogleJsonException: the local copy message must have path set.
    ... 20 common frames omitted
2017-11-06 22:48:12,846 INFO  - $h [UUID(34df5fa6)]: Copying workflow logs from /cromwell-workflow-logs/workflow.34df5fa6-9535-4c3d-913e-a4063cac6e7c.log to gs://fc-f300546b-ca71-489e-ba0c-38f33fc5e19f/29ede9fb-693f-44d7-aef7-a8a002c09188/workflow.logs/workflow.34df5fa6-9535-4c3d-913e-a4063cac6e7c.log

Workspace: nci-cbao-bi-org/BN10_WGS_Chunyang_Analysis
Workflow ID: 29ede9fb-693f-44d7-aef7-a8a002c09188

Best,
Chunyang

Best Answer

  • cbaocbao Member, Broadie
    Accepted Answer

    Hi,

    I fixed it by myself.

    It seems that “” is not an acceptable value for FC in my WDL:
    File? normal_het_allelic_counts = if defined(normal_allelic_counts) then "${output_dir_}/${entity_id}.hets.normal.tsv" else ""

    So, my solution is:
    File? normal_het_allelic_counts = if defined(normal_allelic_counts) then "${output_dir_}/${entity_id}.hets.normal.tsv" else "${output_dir_}/${entity_id}.hets.tsv"

    Then, I can run the pipeline without any issues.

    Thank you!

    Best,
    Chunyang

Answers

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