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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
via GitHub by knoblett
, 1 year ago
Could not localize /foo/bar/baz -> /home/conradL/cromwell-executions/badLocalization/8c7774be-7917-4c6a-88c4-55e495bbb9ec/call-BillyBob/foo/bar/baz
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$$anonfun$localize$1$3.apply(SharedFileSystem.scala:243)	at cromwell.engine.backend.local.SharedFileSystem$$anonfun$localize$1$3.apply(SharedFileSystem.scala:243)	at scala.Option.getOrElse(Option.scala:121)	at cromwell.engine.backend.local.SharedFileSystem$class.localize$1(SharedFileSystem.scala:242)	at cromwell.engine.backend.local.SharedFileSystem$class.adjustFile$1(SharedFileSystem.scala:264)	at cromwell.engine.backend.local.SharedFileSystem$class.localizeWdlValue(SharedFileSystem.scala:271)	at cromwell.engine.backend.sge.SgeBackend.localizeWdlValue(SgeBackend.scala:60)	at cromwell.engine.backend.local.SharedFileSystem$$anonfun$16.apply(SharedFileSystem.scala:223)	at cromwell.engine.backend.local.SharedFileSystem$$anonfun$16.apply(SharedFileSystem.scala:223)	at cromwell.engine.backend.local.SharedFileSystem$$anonfun$17.apply(SharedFileSystem.scala:225)	at cromwell.engine.backend.local.SharedFileSystem$$anonfun$17.apply(SharedFileSystem.scala:224)	at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:245)	at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:245)	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)	at scala.collection.TraversableLike$class.map(TraversableLike.scala:245)	at scala.collection.AbstractTraversable.map(Traversable.scala:104)	at cromwell.engine.backend.local.SharedFileSystem$class.adjustSharedInputPaths(SharedFileSystem.scala:224)	at cromwell.engine.backend.sge.SgeBackend.adjustSharedInputPaths(SgeBackend.scala:60)	at cromwell.engine.backend.sge.SgeBackend.adjustInputPaths(SgeBackend.scala:67)	at cromwell.engine.backend.sge.SgeBackend.instantiateCommand(SgeBackend.scala:260)	at cromwell.engine.backend.BackendCallJobDescriptor.instantiateCommand$lzycompute(JobDescriptor.scala:52)	at cromwell.engine.backend.BackendCallJobDescriptor.instantiateCommand(JobDescriptor.scala:52)	at cromwell.engine.backend.sge.SgeBackend$$anonfun$execute$1.apply(SgeBackend.scala:84)	at cromwell.engine.backend.sge.SgeBackend$$anonfun$execute$1.apply(SgeBackend.scala:82)	at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)	at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)	at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)	at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)	at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)	at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)