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not-working mutect2 WDL pipeline.

prosiumprosium Member
edited May 2018 in Ask the GATK team

I got an error message from the beginning as a WDL novice.
What should i do?

[[email protected] WDL]# java -jar womtool-32.jar inputs mutect2.wdl > mutect2_inputs.json
[[email protected] WDL]# java -jar cromwell-31.jar run mutect2.wdl --inputs mutect2_inputs.json

[2018-05-29 10:46:11,89] [info] Running with database db.url = jdbc:hsqldb:mem:4e696efa-2225-48f8-bdf2-ea0b5f784454;shutdown=false;hsqldb.tx=mvcc
[2018-05-29 10:46:18,90] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-05-29 10:46:18,92] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-05-29 10:46:19,34] [info] Running with database db.url = jdbc:hsqldb:mem:c4a0009a-0d36-4482-9e15-122ccf5ec4a1;shutdown=false;hsqldb.tx=mvcc
[2018-05-29 10:46:20,46] [info] Slf4jLogger started
[2018-05-29 10:46:20,67] [info] Metadata summary refreshing every 2 seconds.
[2018-05-29 10:46:20,69] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2018-05-29 10:46:20,69] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-05-29 10:46:20,70] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-05-29 10:46:21,80] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2018-05-29 10:46:21,82] [info] SingleWorkflowRunnerActor: Submitting workflow
[2018-05-29 10:46:21,86] [info] WDL (Unspecified version) workflow ded52d42-d379-45fb-bd97-22e92dcc4874 submitted
[2018-05-29 10:46:21,86] [info] SingleWorkflowRunnerActor: Workflow submitted ded52d42-d379-45fb-bd97-22e92dcc4874
[2018-05-29 10:46:21,86] [info] 1 new workflows fetched
[2018-05-29 10:46:21,86] [info] WorkflowManagerActor Starting workflow ded52d42-d379-45fb-bd97-22e92dcc4874
[2018-05-29 10:46:21,87] [info] WorkflowManagerActor Successfully started WorkflowActor-ded52d42-d379-45fb-bd97-22e92dcc4874
[2018-05-29 10:46:21,87] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2018-05-29 10:46:28,46] [error] WorkflowManagerActor Workflow ded52d42-d379-45fb-bd97-22e92dcc4874 failed (during MaterializingWorkflowDescriptorState): Workflow input processing failed:
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Float (optional, default = 2.25)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
For input string: "Int? (optional)"
For input string: "Int"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
No coercion defined from '"Array[String]? (optional)"' of type 'spray.json.JsString' to 'Array[String]?'.
For input string: "Int? (optional)"
For input string: "Int? (optional)"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
No coercion defined from '"Array[String]? (optional)"' of type 'spray.json.JsString' to 'Array[String]?'.
For input string: "Int? (optional)"
For input string: "Int? (optional)"
No coercion defined from '"Array[String]? (optional)"' of type 'spray.json.JsString' to 'Array[String]?'.
For input string: "Int? (optional)"
No coercion defined from '"Array[String]? (optional)"' of type 'spray.json.JsString' to 'Array[String]?'.
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
For input string: "Float (optional, default = 2.0)"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
For input string: "Int? (optional)"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing failed:
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Float (optional, default = 2.25)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
For input string: "Int? (optional)"
For input string: "Int"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
No coercion defined from '"Array[String]? (optional)"' of type 'spray.json.JsString' to 'Array[String]?'.
For input string: "Int? (optional)"
For input string: "Int? (optional)"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
No coercion defined from '"Array[String]? (optional)"' of type 'spray.json.JsString' to 'Array[String]?'.
For input string: "Int? (optional)"
For input string: "Int? (optional)"
No coercion defined from '"Array[String]? (optional)"' of type 'spray.json.JsString' to 'Array[String]?'.
For input string: "Int? (optional)"
No coercion defined from '"Array[String]? (optional)"' of type 'spray.json.JsString' to 'Array[String]?'.
For input string: "Int? (optional)"
For input string: "Int? (optional)"
For input string: "Int? (optional)"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
For input string: "Float (optional, default = 2.0)"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
For input string: "Int? (optional)"
No coercion defined from '"Boolean? (optional)"' of type 'spray.json.JsString' to 'Boolean?'.
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.cromwell$engine$workflow$lifecycle$materialization$MaterializeWorkflowDescriptorActor$$workflowInitializationFailed(MaterializeWorkflowDescriptorActor.scala:203)
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:173)
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:168)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
at akka.actor.FSM.processEvent(FSM.scala:665)
at akka.actor.FSM.processEvent$(FSM.scala:662)
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.akka$actor$LoggingFSM$$super$processEvent(MaterializeWorkflowDescriptorActor.scala:126)
at akka.actor.LoggingFSM.processEvent(FSM.scala:801)
at akka.actor.LoggingFSM.processEvent$(FSM.scala:783)
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.processEvent(MaterializeWorkflowDescriptorActor.scala:126)
at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:659)
at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:653)
at akka.actor.Actor.aroundReceive(Actor.scala:514)
at akka.actor.Actor.aroundReceive$(Actor.scala:512)
at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.aroundReceive(MaterializeWorkflowDescriptorActor.scala:126)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:527)
at akka.actor.ActorCell.invoke(ActorCell.scala:496)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
at akka.dispatch.Mailbox.run(Mailbox.scala:224)
at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
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)

[2018-05-29 10:46:28,47] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-05-29 10:46:28,47] [info] Using noop to send events.
[2018-05-29 10:46:28,49] [info] WorkflowManagerActor WorkflowActor-ded52d42-d379-45fb-bd97-22e92dcc4874 is in a terminal state: WorkflowFailedState
[2018-05-29 10:46:32,39] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2018-05-29 10:46:35,73] [info] Message [cromwell.services.loadcontroller.LoadControllerService$LoadMetric] from Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor/ServiceRegistryActor/LoadController/$a#186929977] to Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor/ServiceRegistryActor#-1164453928] was not delivered. [1] dead letters encountered. This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.
[2018-05-29 10:46:35,73] [info] Message [cromwell.services.instrumentation.InstrumentationService$InstrumentationServiceMessage] from Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor/ServiceRegistryActor/LoadController/$a#186929977] to Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor/ServiceRegistryActor#-1164453928] was not delivered. [2] dead letters encountered. This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.
[2018-05-29 10:46:35,73] [info] Message [akka.actor.FSM$Transition] from Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor/ServiceRegistryActor/MetadataService/WriteMetadataActor#-207065173] to Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor#-1602692065] was not delivered. [3] dead letters encountered. This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.
[2018-05-29 10:46:35,73] [info] Message [cromwell.core.actor.StreamActorHelper$StreamFailed] without sender to Actor[akka://cromwell-system/deadLetters] was not delivered. [4] dead letters encountered. This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.
[2018-05-29 10:46:35,73] [info] Message [cromwell.core.actor.StreamActorHelper$StreamFailed] without sender to Actor[akka://cromwell-system/deadLetters] was not delivered. [5] dead letters encountered. This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.
[2018-05-29 10:46:35,73] [info] Message [cromwell.core.actor.StreamActorHelper$StreamFailed] without sender to Actor[akka://cromwell-system/deadLetters] was not delivered. [6] dead letters encountered. This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.
[2018-05-29 10:46:35,74] [error] Outgoing request stream error
akka.stream.AbruptTerminationException: Processor actor [Actor[akka://cromwell-system/user/StreamSupervisor-1/flow-3-0-mergePreferred#930409307]] terminated abruptly
[2018-05-29 10:46:35,74] [error] Outgoing request stream error
akka.stream.AbruptTerminationException: Processor actor [Actor[akka://cromwell-system/user/StreamSupervisor-1/flow-7-0-mergePreferred#1657971584]] terminated abruptly
Workflow ded52d42-d379-45fb-bd97-22e92dcc4874 transitioned to state Failed
[2018-05-29 10:46:35,79] [info] Automatic shutdown of the async connection
[2018-05-29 10:46:35,79] [info] Gracefully shutdown sentry threads.
[2018-05-29 10:46:35,79] [info] Shutdown finished.

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