java.lang.IllegalArgumentException: null

GitHub | mcovarr | 3 months ago
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  1. 0

    GitHub comment 25#257929441

    GitHub | 6 months ago | adamstruck
    java.lang.UnsupportedOperationException: Could not evaluate expression: "-" + args
  2. 0

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

    GitHub | 3 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.IllegalArgumentException

      null

      at sun.nio.fs.UnixPath.subpath()
    2. Java RT
      UnixPath.subpath
      1. sun.nio.fs.UnixPath.subpath(UnixPath.java:346)
      2. sun.nio.fs.UnixPath.subpath(UnixPath.java:43)
      2 frames
    3. cromwell.backend.io
      JobPathsWithDocker.toDockerPath
      1. cromwell.backend.io.JobPathsWithDocker.toDockerPath(JobPathsWithDocker.scala:35)
      1 frame
    4. cromwell.backend.sfs
      SharedFileSystemAsyncJobExecutionActor$class.toUnixPath
      1. cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor$class.toUnixPath(SharedFileSystemAsyncJobExecutionActor.scala:107)
      1 frame
    5. cromwell.backend.impl
      BackgroundConfigAsyncJobExecutionActor.toUnixPath
      1. cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.toUnixPath(ConfigAsyncJobExecutionActor.scala:113)
      1 frame
    6. cromwell.backend.sfs
      SharedFileSystemAsyncJobExecutionActor$$anonfun$commandLineValueMapper$1.apply
      1. cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor$$anonfun$commandLineValueMapper$1.apply(SharedFileSystemAsyncJobExecutionActor.scala:127)
      2. cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor$$anonfun$commandLineValueMapper$1.apply(SharedFileSystemAsyncJobExecutionActor.scala:127)
      2 frames
    7. wdl4s.command
      ParameterCommandPart.instantiate
      1. wdl4s.command.ParameterCommandPart.instantiate(ParameterCommandPart.scala:55)
      1 frame
    8. wdl4s
      Task$$anonfun$instantiateCommand$1$$anonfun$apply$2.apply
      1. wdl4s.Task$$anonfun$instantiateCommand$1$$anonfun$apply$2.apply(Task.scala:108)
      2. wdl4s.Task$$anonfun$instantiateCommand$1$$anonfun$apply$2.apply(Task.scala:108)
      2 frames
    9. Scala
      AbstractTraversable.map
      1. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
      2. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
      3. scala.collection.Iterator$class.foreach(Iterator.scala:893)
      4. scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
      5. scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
      6. scala.collection.AbstractIterable.foreach(Iterable.scala:54)
      7. scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
      8. scala.collection.AbstractTraversable.map(Traversable.scala:104)
      8 frames
    10. wdl4s
      Task$$anonfun$instantiateCommand$1.apply
      1. wdl4s.Task$$anonfun$instantiateCommand$1.apply(Task.scala:108)
      2. wdl4s.Task$$anonfun$instantiateCommand$1.apply(Task.scala:108)
      2 frames
    11. Scala
      Try$.apply
      1. scala.util.Try$.apply(Try.scala:192)
      1 frame
    12. wdl4s
      Task.instantiateCommand
      1. wdl4s.Task.instantiateCommand(Task.scala:108)
      1 frame
    13. cromwell.backend.wdl
      Command$$anonfun$instantiate$1.apply
      1. cromwell.backend.wdl.Command$$anonfun$instantiate$1.apply(Command.scala:28)
      2. cromwell.backend.wdl.Command$$anonfun$instantiate$1.apply(Command.scala:27)
      2 frames
    14. Scala
      Success.flatMap
      1. scala.util.Success.flatMap(Try.scala:231)
      1 frame
    15. cromwell.backend.wdl
      Command$.instantiate
      1. cromwell.backend.wdl.Command$.instantiate(Command.scala:27)
      1 frame
    16. cromwell.backend.standard
      StandardAsyncExecutionActor$class.instantiatedCommand
      1. cromwell.backend.standard.StandardAsyncExecutionActor$class.instantiatedCommand(StandardAsyncExecutionActor.scala:80)
      1 frame
    17. cromwell.backend.impl
      BackgroundConfigAsyncJobExecutionActor.instantiatedCommand
      1. cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:113)
      2. cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:113)
      2 frames
    18. cromwell.backend.sfs
      SharedFileSystemAsyncJobExecutionActor$class.execute
      1. cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor$class.execute(SharedFileSystemAsyncJobExecutionActor.scala:130)
      1 frame
    19. cromwell.backend.impl
      BackgroundConfigAsyncJobExecutionActor.execute
      1. cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:113)
      1 frame
    20. cromwell.backend.standard
      StandardAsyncExecutionActor$$anonfun$executeOrRecover$2.apply
      1. cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$executeOrRecover$2.apply(StandardAsyncExecutionActor.scala:264)
      2. cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$executeOrRecover$2.apply(StandardAsyncExecutionActor.scala:258)
      2 frames
    21. Scala
      Try$.apply
      1. scala.util.Try$.apply(Try.scala:192)
      1 frame
    22. cromwell.backend.standard
      StandardAsyncExecutionActor$class.executeOrRecover
      1. cromwell.backend.standard.StandardAsyncExecutionActor$class.executeOrRecover(StandardAsyncExecutionActor.scala:258)
      1 frame
    23. cromwell.backend.impl
      BackgroundConfigAsyncJobExecutionActor.executeOrRecover
      1. cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:113)
      1 frame
    24. cromwell.backend.async
      AsyncBackendJobExecutionActor$$anonfun$cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover$1.apply
      1. cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover$1.apply(AsyncBackendJobExecutionActor.scala:56)
      2. cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover$1.apply(AsyncBackendJobExecutionActor.scala:56)
      2 frames
    25. cromwell.core.retry
      Retry$.withRetry
      1. cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
      1 frame
    26. cromwell.backend.async
      AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse
      1. cromwell.backend.async.AsyncBackendJobExecutionActor$class.withRetry(AsyncBackendJobExecutionActor.scala:52)
      2. cromwell.backend.async.AsyncBackendJobExecutionActor$class.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:56)
      3. cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:80)
      3 frames
    27. Scala
      PartialFunction$OrElse.applyOrElse
      1. scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:171)
      1 frame
    28. Akka Actor
      Actor$class.aroundReceive
      1. akka.actor.Actor$class.aroundReceive(Actor.scala:496)
      1 frame
    29. cromwell.backend.impl
      BackgroundConfigAsyncJobExecutionActor.aroundReceive
      1. cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:113)
      1 frame
    30. Akka Actor
      Mailbox.exec
      1. akka.actor.ActorCell.receiveMessage(ActorCell.scala:526)
      2. akka.actor.ActorCell.invoke(ActorCell.scala:495)
      3. akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
      4. akka.dispatch.Mailbox.run(Mailbox.scala:224)
      5. akka.dispatch.Mailbox.exec(Mailbox.scala:234)
      5 frames
    31. Scala
      ForkJoinWorkerThread.run
      1. scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
      2. scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
      3. scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
      4. scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
      4 frames