To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits
LATEST RELEASE: FireCloud's latest release was on February 13th. Release Notes can be found 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

Sign In or Register to comment.