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WDLRunner execution failed though pipeline works fine on FireCloud

bshifawbshifaw Member, Broadie, Moderator admin

I want to run the $5 pipeline using wdlrunner but the pipe fails at Haplotypecaller with :

2019-01-17 15:31:09,599 cromwell-system-akka.dispatchers.engine-dispatcher-610 ERROR - WorkflowManagerActor Workflow 9983b240-d08e-4799-ab25-5a41cc0afb73 failed (during ExecutingWorkflowState): java.lang.Exception: Task germline_single_sample_workflow.HaplotypeCaller4:46:1 failed. The job was stopped before the command finished. PAPI error code 2. Execution failed: pulling image: docker pull: running ["docker" "pull" "us.gcr.io/broad-gatk/[email protected]:fd8e7a9e65e6a981ab3b92305492d54c3baef7a803ec3fcb895e5ebeedf824e7"]: exit status 1 (standard error: "failed to register layer: Error processing tar file(exit status 1): write /opt/miniconda/pkgs/mkl-2018.0.1-h19d6760_4.tar.bz2: no space left on device\n")
    at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor$.StandardException(PipelinesApiAsyncBackendJobExecutionActor.scala:79)
    at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.handleFailedRunStatus$1(PipelinesApiAsyncBackendJobExecutionActor.scala:585)
    at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.handleExecutionFailure(PipelinesApiAsyncBackendJobExecutionActor.scala:592)
    at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.handleExecutionFailure(PipelinesApiAsyncBackendJobExecutionActor.scala:83)
    at cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$handleExecutionResult$5.applyOrElse(StandardAsyncExecutionActor.scala:1099)
    at cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$handleExecutionResult$5.applyOrElse(StandardAsyncExecutionActor.scala:1095)
    at scala.concurrent.Future.$anonfun$recoverWith$1(Future.scala:413)
    at scala.concurrent.impl.Promise.$anonfun$transformWith$1(Promise.scala:37)
    at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:60)
    at akka.dispatch.BatchingExecutor$AbstractBatch.processBatch(BatchingExecutor.scala:55)
    at akka.dispatch.BatchingExecutor$BlockableBatch.$anonfun$run$1(BatchingExecutor.scala:91)
    at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:12)
    at scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:81)
    at akka.dispatch.BatchingExecutor$BlockableBatch.run(BatchingExecutor.scala:91)
    at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
    at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
    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)

The exact same wdl and json (method config) works fine on Firecloud, what's causing wdlrunner to fail?

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