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When I use CromWell to run a WDL, I got error like Docker lookup failed

Here is my command:

java -Dconfig.file=myCromwell.conf -jar cromwell-34.jar run processing-for-variant-discovery-gatk4.wdl --inputs input.json

I got following errors:

[warn] BackendPreparationActor_for_70084e86:PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem:3:1 [70084e86]: Docker lookup failed
java.lang.Exception: Failed to get docker hash for broadinstitute/genomes-in-the-cloud:2.3.1-1512499786 Connection failed.
at cromwell.engine.workflow.WorkflowDockerLookupActor.cromwell$engine$workflow$WorkflowDockerLookupActor$$handleLookupFailure(WorkflowDockerLookupActor.scala:196)
at cromwell.engine.workflow.WorkflowDockerLookupActor$$anonfun$3.applyOrElse(WorkflowDockerLookupActor.scala:94)
at cromwell.engine.workflow.WorkflowDockerLookupActor$$anonfun$3.applyOrElse(WorkflowDockerLookupActor.scala:78)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
at akka.actor.FSM.processEvent(FSM.scala:670)
at akka.actor.FSM.processEvent$(FSM.scala:667)
at cromwell.engine.workflow.WorkflowDockerLookupActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowDockerLookupActor.scala:39)
at akka.actor.LoggingFSM.processEvent(FSM.scala:806)
at akka.actor.LoggingFSM.processEvent$(FSM.scala:788)
at cromwell.engine.workflow.WorkflowDockerLookupActor.processEvent(WorkflowDockerLookupActor.scala:39)
at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:664)
at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:658)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
at cromwell.docker.DockerClientHelper$$anonfun$dockerResponseReceive$1.applyOrElse(DockerClientHelper.scala:16)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:171)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at akka.actor.Actor.aroundReceive(Actor.scala:517)
at akka.actor.Actor.aroundReceive$(Actor.scala:515)
at cromwell.engine.workflow.WorkflowDockerLookupActor.aroundReceive(WorkflowDockerLookupActor.scala:39)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
at akka.actor.ActorCell.invoke(ActorCell.scala:557)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
at akka.dispatch.Mailbox.run(Mailbox.scala:225)
at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

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Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @cindylanzao

    I am moving this to the firecloud team forum and @SChaluvadi will be able to help you out with it.

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    @cindylanzao I have asked the development team to take a look, but it may just be a network connection issue. The first error that pops up is "Connection Failed". Have you retried it?

  • mcovarrmcovarr Cambridge, MAMember, Broadie, Dev ✭✭
    edited January 14

    Hi @cindylanzao It looks like Cromwell failed to connect to Docker Hub to get the digest of that Docker image for some reason. This is actually not an error but a warning, although it does mean that the affected job(s) would not be eligible for call caching as a result. Out of curiosity are you able to "docker pull" that image from the machine on which this was running?

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