Jolleboll
commented
2 years ago I think maybe it is related to whether there are batches in the batch table file that have no samples in the sample table file.
Closed Jolleboll closed 1 year ago
Jolleboll
commented
2 years ago I think maybe it is related to whether there are batches in the batch table file that have no samples in the sample table file.
Error message:
[2022-04-27 11:50:34,79] [info] BackgroundConfigAsyncJobExecutionActor [e38dbc61mocha.gtc_tsv:NA:1]: job id: 22366 [2022-04-27 11:50:34,79] [info] BackgroundConfigAsyncJobExecutionActor [e38dbc61mocha.gtc_tsv:NA:1]: Status change from - to Done [2022-04-27 11:50:35,16] [info] WorkflowManagerActor: Workflow e38dbc61-b064-4141-9c6a-e5d54d6dd2f3 failed (during ExecutingWorkflowState): java.lang.RuntimeException: Failed to evaluate 'if_condition' (reason 1 of 1): Evaluating (length(idx2gtc2vcf_files[idx]) > 1) failed: Bad Map access idx2gtc2vcf_files[idx]: This Map[Int, Array[String]] does not have a Int index value [5] at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.processRunnable(ExpressionKey.scala:29) at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.$anonfun$startRunnableNodes$7(WorkflowExecutionActor.scala:563) at scala.collection.immutable.List.map(List.scala:293) at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.cromwell$engine$workflow$lifecycle$execution$WorkflowExecutionActor$$startRunnableNodes(WorkflowExecutionActor.scala:557) at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:211) at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:209) at scala.PartialFunction$OrElse.apply(PartialFunction.scala:172) at akka.actor.FSM.processEvent(FSM.scala:710) at akka.actor.FSM.processEvent$(FSM.scala:704) at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowExecutionActor.scala:54) at akka.actor.LoggingFSM.processEvent(FSM.scala:847) at akka.actor.LoggingFSM.processEvent$(FSM.scala:829) at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.processEvent(WorkflowExecutionActor.scala:54) at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:701) at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:695) at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:38) at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$receive$1.applyOrElse(WorkflowExecutionActor.scala:507) at akka.actor.Actor.aroundReceive(Actor.scala:539) at akka.actor.Actor.aroundReceive$(Actor.scala:537) at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$Timers$$super$aroundReceive(WorkflowExecutionActor.scala:54) at akka.actor.Timers.aroundReceive(Timers.scala:51) at akka.actor.Timers.aroundReceive$(Timers.scala:40) at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.aroundReceive(WorkflowExecutionActor.scala:54) at akka.actor.ActorCell.receiveMessage(ActorCell.scala:614) at akka.actor.ActorCell.invoke(ActorCell.scala:583) at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:268) at akka.dispatch.Mailbox.run(Mailbox.scala:229) at akka.dispatch.Mailbox.exec(Mailbox.scala:241) 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)