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

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Solutions on the web2059

  • via GitHub by Osiris1975
    , 1 year ago
    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
  • Could not localize /foo/bar/baz -> /home/conradL/cromwell-executions/badLocalization/8c7774be-7917-4c6a-88c4-55e495bbb9ec/call-BillyBob/foo/bar/baz
  • Mouse is not implemented yet for the remote WebDriver.
  • Stack trace

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

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