java.lang.RuntimeException: Call aggregate_mafs_workflow.aggregate_mafs:NA:1: return code was 1

GitHub | dheiman | 2 months ago
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  1. 0

    write_lines(Array[File]) creates file with unlocalized file paths

    GitHub | 2 months ago | dheiman
    java.lang.RuntimeException: Call aggregate_mafs_workflow.aggregate_mafs:NA:1: return code was 1
  2. 0

    GitHub comment 1875#274088918

    GitHub | 2 months ago | dheiman
    java.lang.RuntimeException: Call aggregate_mafs_workflow.aggregate_mafs:NA:1: return code was 1
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  4. 0

    Using Local backend, localization of relative symbolic links doesn't work

    GitHub | 2 months ago | delocalizer
    cromwell.backend.sfs.SharedFileSystem$$anonfun$localizeInputs$1$$anon$1: Failures during localization: Could not localize /mnt/lustre/home/conradL/foo/baz -> /mnt/lustre/home/conradL/cromwell-executions/symLinkTest/6cf6c785-dc48-4409-bbd1-6f1411211f42/call-referenceTheLink/inputs/mnt/lustre/home/conradL/foo/baz: /mnt/lustre/home/conradL/bar doesn't exists File not found /mnt/lustre/home/conradL/cromwell-executions/symLinkTest/6cf6c785-dc48-4409-bbd1-6f1411211f42/call-referenceTheLink/inputs/mnt/lustre/home/conradL/foo/baz -> /mnt/lustre/home/conradL/bar File not found /mnt/lustre/home/conradL/bar File not found /mnt/lustre/home/conradL/bar

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    Root Cause Analysis

    1. java.lang.RuntimeException

      Call aggregate_mafs_workflow.aggregate_mafs:NA:1: return code was 1

      at cromwell.backend.standard.StandardAsyncExecutionActor$class.handleExecutionResult()
    2. cromwell.backend.standard
      StandardAsyncExecutionActor$class.handleExecutionResult
      1. cromwell.backend.standard.StandardAsyncExecutionActor$class.handleExecutionResult(StandardAsyncExecutionActor.scala:432)
      1 frame
    3. cromwell.backend.impl
      BackgroundConfigAsyncJobExecutionActor.handleExecutionResult
      1. cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.handleExecutionResult(ConfigAsyncJobExecutionActor.scala:113)
      1 frame
    4. cromwell.backend.standard
      StandardAsyncExecutionActor$class.handlePollSuccess
      1. cromwell.backend.standard.StandardAsyncExecutionActor$class.handlePollSuccess(StandardAsyncExecutionActor.scala:370)
      1 frame
    5. cromwell.backend.impl
      BackgroundConfigAsyncJobExecutionActor.handlePollSuccess
      1. cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.handlePollSuccess(ConfigAsyncJobExecutionActor.scala:113)
      1 frame
    6. cromwell.backend.standard
      StandardAsyncExecutionActor$$anonfun$poll$2.apply
      1. cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$poll$2.apply(StandardAsyncExecutionActor.scala:333)
      2. cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$poll$2.apply(StandardAsyncExecutionActor.scala:332)
      2 frames
    7. Scala
      CallbackRunnable.run
      1. scala.util.Success$$anonfun$map$1.apply(Try.scala:237)
      2. scala.util.Try$.apply(Try.scala:192)
      3. scala.util.Success.map(Try.scala:237)
      4. scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:237)
      5. scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:237)
      6. scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)
      6 frames
    8. Akka Actor
      BatchingExecutor$BlockableBatch$$anonfun$run$1.apply
      1. akka.dispatch.BatchingExecutor$AbstractBatch.processBatch(BatchingExecutor.scala:55)
      2. akka.dispatch.BatchingExecutor$BlockableBatch$$anonfun$run$1.apply$mcV$sp(BatchingExecutor.scala:91)
      3. akka.dispatch.BatchingExecutor$BlockableBatch$$anonfun$run$1.apply(BatchingExecutor.scala:91)
      4. akka.dispatch.BatchingExecutor$BlockableBatch$$anonfun$run$1.apply(BatchingExecutor.scala:91)
      4 frames
    9. Scala
      BlockContext$.withBlockContext
      1. scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:72)
      1 frame
    10. Akka Actor
      ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec
      1. akka.dispatch.BatchingExecutor$BlockableBatch.run(BatchingExecutor.scala:90)
      2. akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:39)
      3. akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:415)
      3 frames
    11. Scala
      ForkJoinWorkerThread.run
      1. scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
      2. scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
      3. scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
      4. scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)[info]
      4 frames