java.lang.UnsupportedOperationException: Could not localize /cil/shed/apps/internal/RNA_utilities/SmartSeq_StarBasedPipeline/scripts/version0.2/SampleData/Mouse-A2-single_S2_L001_R1_001.fastq -> /cil/shed/apps/internal/cromwell/cromwell-executions/smartseq_amr/21612af1-2c5f-400a-a53f-6ac66ec47674/call-RunSTARAlignment/cil/shed/apps/internal/RNA_utilities/SmartSeq_StarBasedPipeline/scripts/version0.2/SampleData/Mouse-A2-single_S2_L001_R1_001.fastq

GitHub | Osiris1975 | 8 months ago
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  1. 0

    Failures during localization

    GitHub | 8 months ago | Osiris1975
    java.lang.UnsupportedOperationException: Could not localize /cil/shed/apps/internal/RNA_utilities/SmartSeq_StarBasedPipeline/scripts/version0.2/SampleData/Mouse-A2-single_S2_L001_R1_001.fastq -> /cil/shed/apps/internal/cromwell/cromwell-executions/smartseq_amr/21612af1-2c5f-400a-a53f-6ac66ec47674/call-RunSTARAlignment/cil/shed/apps/internal/RNA_utilities/SmartSeq_StarBasedPipeline/scripts/version0.2/SampleData/Mouse-A2-single_S2_L001_R1_001.fastq
  2. 0

    Running in server mode, jobs that have localization error become immortal

    GitHub | 9 months ago | knoblett
    java.lang.UnsupportedOperationException: Could not localize /foo/bar/baz -> /home/conradL/cromwell-executions/badLocalization/8c7774be-7917-4c6a-88c4-55e495bbb9ec/call-BillyBob/foo/bar/baz

    Root Cause Analysis

    1. java.lang.UnsupportedOperationException

      Could not localize /cil/shed/apps/internal/RNA_utilities/SmartSeq_StarBasedPipeline/scripts/version0.2/SampleData/Mouse-A2-single_S2_L001_R1_001.fastq -> /cil/shed/apps/internal/cromwell/cromwell-executions/smartseq_amr/21612af1-2c5f-400a-a53f-6ac66ec47674/call-RunSTARAlignment/cil/shed/apps/internal/RNA_utilities/SmartSeq_StarBasedPipeline/scripts/version0.2/SampleData/Mouse-A2-single_S2_L001_R1_001.fastq

      at cromwell.engine.backend.local.SharedFileSystem$$anonfun$localize$1$3.apply()
    2. cromwell.engine.backend
      SharedFileSystem$$anonfun$localize$1$3.apply
      1. cromwell.engine.backend.local.SharedFileSystem$$anonfun$localize$1$3.apply(SharedFileSystem.scala:243)[cromwell-0.19.jar:0.19]
      2. cromwell.engine.backend.local.SharedFileSystem$$anonfun$localize$1$3.apply(SharedFileSystem.scala:243)[cromwell-0.19.jar:0.19]
      2 frames
    3. Scala
      Option.getOrElse
      1. scala.Option.getOrElse(Option.scala:121)[cromwell-0.19.jar:0.19]
      1 frame
    4. cromwell.engine.backend
      SharedFileSystem$$anonfun$17.apply
      1. cromwell.engine.backend.local.SharedFileSystem$class.localize$1(SharedFileSystem.scala:242)[cromwell-0.19.jar:0.19]
      2. cromwell.engine.backend.local.SharedFileSystem$class.adjustFile$1(SharedFileSystem.scala:264)[cromwell-0.19.jar:0.19]
      3. cromwell.engine.backend.local.SharedFileSystem$class.localizeWdlValue(SharedFileSystem.scala:271)[cromwell-0.19.jar:0.19]
      4. cromwell.engine.backend.sge.SgeBackend.localizeWdlValue(SgeBackend.scala:60)[cromwell-0.19.jar:0.19]
      5. cromwell.engine.backend.local.SharedFileSystem$$anonfun$16.apply(SharedFileSystem.scala:223)[cromwell-0.19.jar:0.19]
      6. cromwell.engine.backend.local.SharedFileSystem$$anonfun$16.apply(SharedFileSystem.scala:223)[cromwell-0.19.jar:0.19]
      7. cromwell.engine.backend.local.SharedFileSystem$$anonfun$17.apply(SharedFileSystem.scala:225)[cromwell-0.19.jar:0.19]
      8. cromwell.engine.backend.local.SharedFileSystem$$anonfun$17.apply(SharedFileSystem.scala:224)[cromwell-0.19.jar:0.19]
      8 frames
    5. Scala
      AbstractTraversable.map
      1. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:245)[cromwell-0.19.jar:0.19]
      2. scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:245)[cromwell-0.19.jar:0.19]
      3. scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)[cromwell-0.19.jar:0.19]
      4. scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)[cromwell-0.19.jar:0.19]
      5. scala.collection.TraversableLike$class.map(TraversableLike.scala:245)[cromwell-0.19.jar:0.19]
      6. scala.collection.AbstractTraversable.map(Traversable.scala:104)[cromwell-0.19.jar:0.19]
      6 frames
    6. cromwell.engine.backend
      SgeBackend$$anonfun$execute$1.apply
      1. cromwell.engine.backend.local.SharedFileSystem$class.adjustSharedInputPaths(SharedFileSystem.scala:224)[cromwell-0.19.jar:0.19]
      2. cromwell.engine.backend.sge.SgeBackend.adjustSharedInputPaths(SgeBackend.scala:60)[cromwell-0.19.jar:0.19]
      3. cromwell.engine.backend.sge.SgeBackend.adjustInputPaths(SgeBackend.scala:67)[cromwell-0.19.jar:0.19]
      4. cromwell.engine.backend.sge.SgeBackend.instantiateCommand(SgeBackend.scala:260)[cromwell-0.19.jar:0.19]
      5. cromwell.engine.backend.BackendCallJobDescriptor.instantiateCommand$lzycompute(JobDescriptor.scala:52)[cromwell-0.19.jar:0.19]
      6. cromwell.engine.backend.BackendCallJobDescriptor.instantiateCommand(JobDescriptor.scala:52)[cromwell-0.19.jar:0.19]
      7. cromwell.engine.backend.sge.SgeBackend$$anonfun$execute$1.apply(SgeBackend.scala:84)[cromwell-0.19.jar:0.19]
      8. cromwell.engine.backend.sge.SgeBackend$$anonfun$execute$1.apply(SgeBackend.scala:82)[cromwell-0.19.jar:0.19]
      8 frames
    7. Scala
      Future$PromiseCompletingRunnable.run
      1. scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)[cromwell-0.19.jar:0.19]
      2. scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)[cromwell-0.19.jar:0.19]
      2 frames
    8. Akka Actor
      ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec
      1. akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)[cromwell-0.19.jar:0.19]
      2. akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)[cromwell-0.19.jar:0.19]
      2 frames
    9. Scala
      ForkJoinWorkerThread.run
      1. scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)[cromwell-0.19.jar:0.19]
      2. scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)[cromwell-0.19.jar:0.19]
      3. scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)[cromwell-0.19.jar:0.19]
      4. scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)[cromwell-0.19.jar:0.19]
      4 frames