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[ERROR] the local copy message must have path set.
cbao
Member, Broadie ✭✭
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 - $h [UUID(34df5fa6)]: Copying workflow logs from /cromwell-workflow-logs/workflow.34df5fa6-9535-4c3d-913e-a4063cac6e7c.log to gs://fc-f300546b-ca71-489e-ba0c-38f33fc5e19f/29ede9fb-693f-44d7-aef7-a8a002c09188/workflow.logs/workflow.34df5fa6-9535-4c3d-913e-a4063cac6e7c.log
Workspace: nci-cbao-bi-org/BN10_WGS_Chunyang_Analysis
Workflow ID: 29ede9fb-693f-44d7-aef7-a8a002c09188
Best,
Chunyang
Best Answer
-
cbao
✭✭
Hi,
I fixed it by myself.
It seems that “” is not an acceptable value for FC in my WDL:
File? normal_het_allelic_counts = if defined(normal_allelic_counts) then "${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_}/${entity_id}.hets.tsv"Then, I can run the pipeline without any issues.
Thank you!
Best,
Chunyang
Answers
I haven't encountered this error before and my initial exploration of your workspace didn't reveal anything obviously wrong. I will ask a developer to take a look and get back to you. Could you share the workspace with [email protected] if you haven't already?
Looking around I found this https://software.broadinstitute.org/wdl/documentation/article?issue=2367&repo=cromwell and I can't see your WDL, but I see one of the inputs is called gatk_jar and the value is /gatk/gatk.jar - which is not a google bucket path - if gatk_jar is a File input in your WDL, that will need to be the URL to a that file in a bucket you have access to
Thank you! @abaumann and @KateN
But, /gatk/gatk.jar is a absolute path in my docker image. I suppose that it is a issue of cromwell for reading a optional argument in Java.
Thanks @KateN
I shared. The method is
cnv_somatic_pair_workflow_cbao
Could you also give me access to the WDL?
Hi @abaumann
Thank you! I will email you directly. It's a gatk4 pipeline. I am not allowed to post here.
Hi,
I fixed it by myself.
It seems that “” is not an acceptable value for FC in my WDL:
File? normal_het_allelic_counts = if defined(normal_allelic_counts) then "${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