AWS and GCP error parsing WDL with "Unrecognized token"

Hi,

I have tried a very simple WDL script for testing on both AWS and GCP cloud platforms with Cromwell v37. The WDL script is a simple "Hello World" test WDL:

task hello {
  String name = "World"

  command {
    echo 'Hello, ${name}!'
  }
  output {
    File response = stdout()
  }
}

workflow test {
  call hello
}

The WDL executes correctly locally. However, I get the following error on both AWS and GCP:

2019-01-03 03:01:42,810 cromwell-system-akka.actor.default-dispatcher-470402 WARN - Illegal header: Illegal 'user-agent' header: Invalid input '/', expected OWS, 'EOI', tchar, product-or-comment or comment (line 1, column 55): Mozilla/5.0(WindowsNT6.1;rv:31.0)Gecko/20100101Firefox/31.0
^
2019-01-03 07:16:31,515 cromwell-system-akka.actor.default-dispatcher-474513 WARN - Illegal header: Illegal 'user-agent' header: Invalid input '/', expected OWS, 'EOI', tchar, product-or-comment or comment (line 1, column 55): Mozilla/5.0(WindowsNT6.1;rv:31.0)Gecko/20100101Firefox/31.0
^
2019-01-03 15:46:53,038 cromwell-system-akka.actor.default-dispatcher-480234 WARN - Illegal header: Illegal 'user-agent' header: Invalid input '/', expected OWS, 'EOI', tchar, product-or-comment or comment (line 1, column 55): Mozilla/5.0(WindowsNT6.1;rv:31.0)Gecko/20100101Firefox/31.0
^
2019-01-03 19:42:42,552 cromwell-system-akka.dispatchers.api-dispatcher-466028 INFO - WDL (1.0) workflow 48abf831-6811-49c1-a450-b73a32b3f8bd submitted
2019-01-03 19:42:52,282 cromwell-system-akka.dispatchers.engine-dispatcher-25 INFO - 1 new workflows fetched
2019-01-03 19:42:52,282 cromwell-system-akka.dispatchers.engine-dispatcher-25 INFO - WorkflowManagerActor Starting workflow UUID(48abf831-6811-49c1-a450-b73a32b3f8bd)
2019-01-03 19:42:52,282 cromwell-system-akka.dispatchers.engine-dispatcher-25 INFO - WorkflowManagerActor Successfully started WorkflowActor-48abf831-6811-49c1-a450-b73a32b3f8bd
2019-01-03 19:42:52,282 cromwell-system-akka.dispatchers.engine-dispatcher-25 INFO - Retrieved 1 workflows from the WorkflowStoreActor
2019-01-03 19:42:52,287 cromwell-system-akka.dispatchers.engine-dispatcher-21 INFO - MaterializeWorkflowDescriptorActor [UUID(48abf831)]: Parsing workflow as WDL 1.0
2019-01-03 19:42:52,293 cromwell-system-akka.dispatchers.engine-dispatcher-27 ERROR - WorkflowManagerActor Workflow 48abf831-6811-49c1-a450-b73a32b3f8bd failed (during MaterializingWorkflowDescriptorState): cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing failed:
Unrecognized token on line 1, column 1:
task hello {
^
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.cromwell$engine$workflow$lifecycle$materialization$MaterializeWorkflowDescriptorActor$$workflowInitializationFailed(MaterializeWorkflowDescriptorActor.scala:214)
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:184)
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:179)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
at akka.actor.FSM.processEvent(FSM.scala:684)
at akka.actor.FSM.processEvent$(FSM.scala:681)
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.akka$actor$LoggingFSM$$super$processEvent(MaterializeWorkflowDescriptorActor.scala:135)
at akka.actor.LoggingFSM.processEvent(FSM.scala:820)
at akka.actor.LoggingFSM.processEvent$(FSM.scala:802)
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.processEvent(MaterializeWorkflowDescriptorActor.scala:135)
at akka.actor.FSM.akka$actor$FSM$$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.lifecycle.materialization.MaterializeWorkflowDescriptorActor.aroundReceive(MaterializeWorkflowDescriptorActor.scala:135)
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)
2019-01-03 19:42:52,294 cromwell-system-akka.dispatchers.engine-dispatcher-8 INFO - WorkflowManagerActor WorkflowActor-48abf831-6811-49c1-a450-b73a32b3f8bd is in a terminal state: WorkflowFailedState

I had initially tried this with a previously working exome workflow on GCP (complete with Docker invocations, etc.), but the move to v37 seems to have introduced this issue.

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Best Answer

  • decontideconti DFCI
    Accepted Answer

    I solved the issue. The solution was that under the workflowTypeVersion, "1.0" would report a the "Unrecognized token" despite a simple HelloWorld.wdl example. Switching the workflowTypeVersion to "draft-2" will parse the WDL file properly.

    I hope this helps anyone that runs into the same issue.

Answers

  • decontideconti DFCIMember
    Accepted Answer

    I solved the issue. The solution was that under the workflowTypeVersion, "1.0" would report a the "Unrecognized token" despite a simple HelloWorld.wdl example. Switching the workflowTypeVersion to "draft-2" will parse the WDL file properly.

    I hope this helps anyone that runs into the same issue.

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