Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

Error attempting to Execute java.lang.RuntimeException: Cannot build a local path

I'm getting this error message:

2018-12-28 10:06:05,51] [info] Running with database db.url = jdbc:hsqldb:mem:7f85c3ca-a43e-4eae-9eb5-0b2766111e45;shutdown=false;hsqldb.tx=mvcc
[2018-12-28 10:06:33,18] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-12-28 10:06:33,22] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-12-28 10:06:33,69] [info] Running with database db.url = jdbc:hsqldb:mem:af8c85d6-2963-418a-92c2-56aa76057dd9;shutdown=false;hsqldb.tx=mvcc
[2018-12-28 10:06:36,44] [info] Slf4jLogger started
[2018-12-28 10:06:43,38] [info] Workflow heartbeat configuration:
{
  "cromwellId" : "cromid-92be876",
  "heartbeatInterval" : "2 minutes",
  "ttl" : "10 minutes",
  "writeBatchSize" : 10000,
  "writeThreshold" : 10000
}
[2018-12-28 10:06:43,67] [info] Metadata summary refreshing every 2 seconds.
[2018-12-28 10:06:43,95] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-12-28 10:06:43,95] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-12-28 10:06:43,95] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2018-12-28 10:07:07,85] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2018-12-28 10:07:08,34] [info] SingleWorkflowRunnerActor: Version 36
[2018-12-28 10:07:08,49] [info] SingleWorkflowRunnerActor: Submitting workflow
[2018-12-28 10:07:10,05] [info] Unspecified type (Unspecified version) workflow ad045a66-1bad-41c7-9f70-3b7480c3931c submitted
[2018-12-28 10:07:10,22] [info] SingleWorkflowRunnerActor: Workflow submitted ad045a66-1bad-41c7-9f70-3b7480c3931c
[2018-12-28 10:07:10,59] [info] 1 new workflows fetched
[2018-12-28 10:07:10,87] [info] WorkflowManagerActor Starting workflow ad045a66-1bad-41c7-9f70-3b7480c3931c
[2018-12-28 10:07:11,11] [info] WorkflowManagerActor Successfully started WorkflowActor-ad045a66-1bad-41c7-9f70-3b7480c3931c
[2018-12-28 10:07:11,12] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2018-12-28 10:07:11,28] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2018-12-28 10:07:12,06] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData
[2018-12-28 10:07:15,60] [info] MaterializeWorkflowDescriptorActor [ad045a66]: Parsing workflow as WDL draft-2
[2018-12-28 10:07:26,72] [info] MaterializeWorkflowDescriptorActor [ad045a66]: Call-to-Backend assignments: helloMethylationPipeline.MethylationPipeline -> Local
[2018-12-28 10:07:28,25] [warn] Local [ad045a66]: Key/s [memory, disks, bootDiskSizeGb] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-12-28 10:07:29,27] [info] Message [cromwell.docker.DockerHashActor$DockerHashSuccessResponse] from Actor[akka://cromwell-system/user/HealthMonitorDockerHashActor#-608644452] to Actor[akka://cromwell-system/deadLetters] was not delivered. [1] dead letters encountered, no more dead letters will be logged. If this is not an expected behavior, then [Actor[akka://cromwell-system/deadLetters]] may have terminated unexpectedly, This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.
[2018-12-28 10:07:32,01] [info] WorkflowExecutionActor-ad045a66-1bad-41c7-9f70-3b7480c3931c [ad045a66]: Starting helloMethylationPipeline.MethylationPipeline
[2018-12-28 10:07:41,68] [warn] BackgroundConfigAsyncJobExecutionActor [ad045a66helloMethylationPipeline.MethylationPipeline:NA:1]: Unrecognized runtime attribute keys: bootDiskSizeGb, disks, memory
[2018-12-28 10:07:43,18] [error] BackgroundConfigAsyncJobExecutionActor [ad045a66helloMethylationPipeline.MethylationPipeline:NA:1]: Error attempting to Execute
java.lang.RuntimeException: Cannot build a local path from C:\Users\Len\Dropbox\Programming\MethylationPipeline\cromwell-executions\helloMethylationPipeline\ad045a66-1bad-41c7-9f70-3b7480c3931c\call-MethylationPipeline\execution
        at cromwell.core.path.DefaultPathBuilder$.$anonfun$build$1(DefaultPathBuilder.scala:32)
        at scala.util.Try$.apply(Try.scala:209)
        at cromwell.core.path.DefaultPathBuilder$.build(DefaultPathBuilder.scala:18)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.$anonfun$mapCommandLineWomFile$1(SharedFileSystemAsyncJobExecutionActor.scala:122)
        at wom.values.WomSingleFile.mapFile(WomFile.scala:220)
        at wom.values.WomSingleFile.mapFile(WomFile.scala:201)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.mapCommandLineWomFile(SharedFileSystemAsyncJobExecutionActor.scala:121)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.mapCommandLineWomFile$(SharedFileSystemAsyncJobExecutionActor.scala:120)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.mapCommandLineWomFile(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$commandLineValueMapper$2(StandardAsyncExecutionActor.scala:161)
        at wom.WomFileMapper$.$anonfun$mapWomFiles$1(WomFileMapper.scala:25)
        at scala.util.Try$.apply(Try.scala:209)
        at wom.WomFileMapper$.mapWomFiles(WomFileMapper.scala:25)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$commandLineValueMapper$1(StandardAsyncExecutionActor.scala:161)
        at mouse.AnyOps$.$bar$greater$extension(any.scala:8)
        at cromwell.backend.standard.StandardAsyncExecutionActor.localize$1(StandardAsyncExecutionActor.scala:400)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$runtimeEnvironmentPathMapper$1(StandardAsyncExecutionActor.scala:401)
        at mouse.AnyOps$.$bar$greater$extension(any.scala:8)
        at cromwell.backend.standard.StandardAsyncExecutionActor.runtimeEnvironmentPathMapper(StandardAsyncExecutionActor.scala:401)
        at cromwell.backend.standard.StandardAsyncExecutionActor.runtimeEnvironmentPathMapper$(StandardAsyncExecutionActor.scala:399)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.runtimeEnvironmentPathMapper(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$runtimeEnvironment$1(StandardAsyncExecutionActor.scala:405)
        at mouse.AnyOps$.$bar$greater$extension(any.scala:8)
        at cromwell.backend.standard.StandardAsyncExecutionActor.runtimeEnvironment(StandardAsyncExecutionActor.scala:405)
        at cromwell.backend.standard.StandardAsyncExecutionActor.runtimeEnvironment$(StandardAsyncExecutionActor.scala:405)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.runtimeEnvironment$lzycompute(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.runtimeEnvironment(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:530)
        at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:500)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:313)
        at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:312)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:151)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:150)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
        at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:134)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:131)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:628)
        at scala.util.Try$.apply(Try.scala:209)
        at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:628)
        at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:628)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:943)
        at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:935)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
        at cromwell.core.retry.Retry$.withRetry(Retry.scala:38)
        at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:61)
        at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:65)
        at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:88)
        at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
        at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
        at akka.actor.Actor.aroundReceive(Actor.scala:517)
        at akka.actor.Actor.aroundReceive$(Actor.scala:515)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:198)
        at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
        at akka.actor.ActorCell.invoke(ActorCell.scala:557)
        at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
        at akka.dispatch.Mailbox.run(Mailbox.scala:225)
        at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
        at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
        at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
        at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
        at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
[2018-12-28 10:07:44,72] [error] WorkflowManagerActor Workflow ad045a66-1bad-41c7-9f70-3b7480c3931c failed (during ExecutingWorkflowState): cromwell.core.CromwellFatalException: java.lang.RuntimeException: Cannot build a local path from C:\Users\Len\Dropbox\Programming\MethylationPipeline\cromwell-executions\helloMethylationPipeline\ad045a66-1bad-41c7-9f70-3b7480c3931c\call-MethylationPipeline\execution
        at cromwell.core.CromwellFatalException$.apply(core.scala:20)
        at cromwell.core.retry.Retry$$anonfun$withRetry$1.applyOrElse(Retry.scala:39)
        at cromwell.core.retry.Retry$$anonfun$withRetry$1.applyOrElse(Retry.scala:38)
        at scala.concurrent.Future.$anonfun$recoverWith$1(Future.scala:413)
        at scala.concurrent.impl.Promise.$anonfun$transformWith$1(Promise.scala:37)
        at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:60)
        at akka.dispatch.BatchingExecutor$AbstractBatch.processBatch(BatchingExecutor.scala:55)
        at akka.dispatch.BatchingExecutor$BlockableBatch.$anonfun$run$1(BatchingExecutor.scala:91)
        at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:12)
        at scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:81)
        at akka.dispatch.BatchingExecutor$BlockableBatch.run(BatchingExecutor.scala:91)
        at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
        at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
        at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
        at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
        at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
        at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: java.lang.RuntimeException: Cannot build a local path from C:\Users\Len\Dropbox\Programming\MethylationPipeline\cromwell-executions\helloMethylationPipeline\ad045a66-1bad-41c7-9f70-3b7480c3931c\call-MethylationPipeline\execution
        at cromwell.core.path.DefaultPathBuilder$.$anonfun$build$1(DefaultPathBuilder.scala:32)
        at scala.util.Try$.apply(Try.scala:209)
        at cromwell.core.path.DefaultPathBuilder$.build(DefaultPathBuilder.scala:18)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.$anonfun$mapCommandLineWomFile$1(SharedFileSystemAsyncJobExecutionActor.scala:122)
        at wom.values.WomSingleFile.mapFile(WomFile.scala:220)
        at wom.values.WomSingleFile.mapFile(WomFile.scala:201)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.mapCommandLineWomFile(SharedFileSystemAsyncJobExecutionActor.scala:121)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.mapCommandLineWomFile$(SharedFileSystemAsyncJobExecutionActor.scala:120)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.mapCommandLineWomFile(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$commandLineValueMapper$2(StandardAsyncExecutionActor.scala:161)
        at wom.WomFileMapper$.$anonfun$mapWomFiles$1(WomFileMapper.scala:25)
        at scala.util.Try$.apply(Try.scala:209)
        at wom.WomFileMapper$.mapWomFiles(WomFileMapper.scala:25)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$commandLineValueMapper$1(StandardAsyncExecutionActor.scala:161)
        at mouse.AnyOps$.$bar$greater$extension(any.scala:8)
        at cromwell.backend.standard.StandardAsyncExecutionActor.localize$1(StandardAsyncExecutionActor.scala:400)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$runtimeEnvironmentPathMapper$1(StandardAsyncExecutionActor.scala:401)
        at mouse.AnyOps$.$bar$greater$extension(any.scala:8)
        at cromwell.backend.standard.StandardAsyncExecutionActor.runtimeEnvironmentPathMapper(StandardAsyncExecutionActor.scala:401)
        at cromwell.backend.standard.StandardAsyncExecutionActor.runtimeEnvironmentPathMapper$(StandardAsyncExecutionActor.scala:399)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.runtimeEnvironmentPathMapper(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$runtimeEnvironment$1(StandardAsyncExecutionActor.scala:405)
        at mouse.AnyOps$.$bar$greater$extension(any.scala:8)
        at cromwell.backend.standard.StandardAsyncExecutionActor.runtimeEnvironment(StandardAsyncExecutionActor.scala:405)
        at cromwell.backend.standard.StandardAsyncExecutionActor.runtimeEnvironment$(StandardAsyncExecutionActor.scala:405)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.runtimeEnvironment$lzycompute(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.runtimeEnvironment(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:530)
        at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:500)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:313)
        at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:312)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:151)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:150)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
        at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:134)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:131)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:628)
        at scala.util.Try$.apply(Try.scala:209)
        at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:628)
        at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:628)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:943)
        at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:935)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:198)
        at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
        at cromwell.core.retry.Retry$.withRetry(Retry.scala:38)
        at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:61)
        at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:65)
        at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:88)
        at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
        at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
        at akka.actor.Actor.aroundReceive(Actor.scala:517)
        at akka.actor.Actor.aroundReceive$(Actor.scala:515)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:198)
        at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
        at akka.actor.ActorCell.invoke(ActorCell.scala:557)
        at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
        at akka.dispatch.Mailbox.run(Mailbox.scala:225)
        at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
        ... 4 more

[2018-12-28 10:07:44,76] [error] Failed to delete workflow log
java.nio.file.FileSystemException: C:\Users\Len\Dropbox\Programming\MethylationPipeline\cromwell-workflow-logs\workflow.ad045a66-1bad-41c7-9f70-3b7480c3931c.log: The process cannot access the file because it is being used by another process.

        at sun.nio.fs.WindowsException.translateToIOException(Unknown Source)
        at sun.nio.fs.WindowsException.rethrowAsIOException(Unknown Source)
        at sun.nio.fs.WindowsException.rethrowAsIOException(Unknown Source)
        at sun.nio.fs.WindowsFileSystemProvider.implDelete(Unknown Source)
        at sun.nio.fs.AbstractFileSystemProvider.delete(Unknown Source)
        at java.nio.file.Files.delete(Unknown Source)
        at better.files.File.delete(File.scala:619)
        at cromwell.core.path.BetterFileMethods.delete(BetterFileMethods.scala:413)
        at cromwell.core.path.BetterFileMethods.delete$(BetterFileMethods.scala:412)
        at cromwell.core.path.DefaultPath.delete(DefaultPathBuilder.scala:55)
        at cromwell.core.logging.WorkflowLogger.$anonfun$close$2(WorkflowLogger.scala:124)
        at cromwell.core.logging.WorkflowLogger.$anonfun$close$2$adapted(WorkflowLogger.scala:123)
        at scala.Option.foreach(Option.scala:257)
        at cromwell.core.logging.WorkflowLogger.$anonfun$close$1(WorkflowLogger.scala:123)
        at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:12)
        at scala.util.Try$.apply(Try.scala:209)
        at cromwell.core.logging.WorkflowLogger.close(WorkflowLogger.scala:123)
        at cromwell.engine.workflow.WorkflowActor$$anonfun$8.applyOrElse(WorkflowActor.scala:448)
        at cromwell.engine.workflow.WorkflowActor$$anonfun$8.applyOrElse(WorkflowActor.scala:413)
        at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
        at akka.actor.FSM.$anonfun$handleTransition$1(FSM.scala:627)
        at akka.actor.FSM.$anonfun$handleTransition$1$adapted(FSM.scala:627)
        at scala.collection.immutable.List.foreach(List.scala:389)
        at akka.actor.FSM.handleTransition(FSM.scala:627)
        at akka.actor.FSM.makeTransition(FSM.scala:709)
        at akka.actor.FSM.makeTransition$(FSM.scala:702)
        at cromwell.engine.workflow.WorkflowActor.makeTransition(WorkflowActor.scala:193)
        at akka.actor.FSM.applyState(FSM.scala:694)
        at akka.actor.FSM.applyState$(FSM.scala:692)
        at cromwell.engine.workflow.WorkflowActor.applyState(WorkflowActor.scala:193)
        at akka.actor.FSM.processEvent(FSM.scala:689)
        at akka.actor.FSM.processEvent$(FSM.scala:681)
        at cromwell.engine.workflow.WorkflowActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowActor.scala:193)
        at akka.actor.LoggingFSM.processEvent(FSM.scala:820)
        at akka.actor.LoggingFSM.processEvent$(FSM.scala:802)
        at cromwell.engine.workflow.WorkflowActor.processEvent(WorkflowActor.scala:193)
        at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:678)
        at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:672)
        at akka.actor.Actor.aroundReceive(Actor.scala:517)
        at akka.actor.Actor.aroundReceive$(Actor.scala:515)
        at cromwell.engine.workflow.WorkflowActor.akka$actor$Timers$$super$aroundReceive(WorkflowActor.scala:193)
        at akka.actor.Timers.aroundReceive(Timers.scala:55)
        at akka.actor.Timers.aroundReceive$(Timers.scala:40)
        at cromwell.engine.workflow.WorkflowActor.aroundReceive(WorkflowActor.scala:193)
        at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
        at akka.actor.ActorCell.invoke(ActorCell.scala:557)
        at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
        at akka.dispatch.Mailbox.run(Mailbox.scala:225)
        at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
        at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
        at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
        at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
        at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
[2018-12-28 10:07:44,76] [info] WorkflowManagerActor WorkflowActor-ad045a66-1bad-41c7-9f70-3b7480c3931c is in a terminal state: WorkflowFailedState
[2018-12-28 10:07:53,72] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2018-12-28 10:07:54,08] [info] Workflow polling stopped
[2018-12-28 10:07:54,19] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2018-12-28 10:07:54,21] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2018-12-28 10:07:54,24] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2018-12-28 10:07:54,26] [info] JobExecutionTokenDispenser stopped
[2018-12-28 10:07:54,26] [info] Aborting all running workflows.
[2018-12-28 10:07:54,27] [info] WorkflowLogCopyRouter stopped
[2018-12-28 10:07:54,29] [info] WorkflowStoreActor stopped
[2018-12-28 10:07:54,29] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2018-12-28 10:07:54,29] [info] WorkflowManagerActor All workflows finished
[2018-12-28 10:07:54,29] [info] WorkflowManagerActor stopped
[2018-12-28 10:07:54,35] [info] Connection pools shut down
[2018-12-28 10:07:54,40] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2018-12-28 10:07:54,40] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2018-12-28 10:07:54,40] [info] SubWorkflowStoreActor stopped
[2018-12-28 10:07:54,40] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2018-12-28 10:07:54,41] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2018-12-28 10:07:54,43] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2018-12-28 10:07:54,43] [info] JobStoreActor stopped
[2018-12-28 10:07:54,43] [info] KvWriteActor Shutting down: 0 queued messages to process
[2018-12-28 10:07:54,43] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2018-12-28 10:07:54,43] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2018-12-28 10:07:54,44] [info] CallCacheWriteActor stopped
[2018-12-28 10:07:54,44] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2018-12-28 10:07:54,51] [info] DockerHashActor stopped
[2018-12-28 10:07:54,51] [info] IoProxy stopped
[2018-12-28 10:07:54,51] [info] ServiceRegistryActor stopped
[2018-12-28 10:07:54,57] [info] Database closed
[2018-12-28 10:07:54,57] [info] Stream materializer shut down
[2018-12-28 10:07:54,58] [info] WDL HTTP import resolver closed
Workflow ad045a66-1bad-41c7-9f70-3b7480c3931c transitioned to state Failed

I'd attach my files but I'm getting a "File format not allowed" error for all of them.

I'm running Cromwell 36 on Windows Subsystem for Linux. I'm guessing WSL is probably causing the issue but I wanted to see if anyone had any insight before I switch to Linux.

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