Hi,
I launched a simple trimming and fastqc WDL to google cloud for processing, but I am always seeing failing messages similar to below. The WDL run fine locally and I have tried running 1 sample successfully in google cloud. What would cause this error message and what does it mean?
[2018-06-26 23:57:28,00] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:4:1]: Status change from - to Running
[2018-06-26 23:57:28,18] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:2:1]: Status change from - to Running
[2018-06-26 23:57:28,18] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:5:1]: Status change from - to Running
[2018-06-26 23:57:28,23] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:7:1]: Status change from - to Running
[2018-06-26 23:57:28,24] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:1:1]: Status change from - to Preempted
[2018-06-26 23:57:28,40] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.trim:3:1]: Status change from Running to Success
[2018-06-26 23:57:32,93] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:6:1]: job id: operations/EJ-xn_TDLBj_qpCc_M6O7UIg1arNpuYFKg9wcm9kdWN0aW9uUXVldWU
[2018-06-26 23:57:32,93] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:9:1]: job id: operations/EI-xn_TDLBjM59rYq7O05mEg1arNpuYFKg9wcm9kdWN0aW9uUXVldWU
[2018-06-26 23:58:02,24] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:9:1]: Status change from - to Initializing
[2018-06-26 23:58:02,25] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:6:1]: Status change from - to Initializing
[2018-06-26 23:59:09,82] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:6:1]: Status change from Initializing to Running
[2018-06-27 00:00:18,21] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:7:1]: Status change from Running to Success
[2018-06-27 00:00:51,80] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:10:1]: Status change from Running to Success
[2018-06-27 00:00:52,14] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:2:1]: Status change from Running to Success
[2018-06-27 00:00:52,14] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:8:1]: Status change from Running to Success
[2018-06-27 00:01:25,70] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:0:1]: Status change from Running to Success
[2018-06-27 00:01:25,86] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:9:1]: Status change from Initializing to Running
[2018-06-27 00:01:59,90] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:5:1]: Status change from Running to Success
[2018-06-27 00:03:40,69] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:6:1]: Status change from Running to Success
[2018-06-27 00:05:55,05] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:9:1]: Status change from Running to Success
[2018-06-27 00:07:02,28] [info] PipelinesApiAsyncBackendJobExecutionActor [05746aafiggygetout_trim_fastqc.postfastqc:4:1]: Status change from Running to Success
[2018-06-27 00:07:05,08] [error] WorkflowManagerActor Workflow 05746aaf-73e5-4a97-8bb4-32fd9deaf6b1 failed (during ExecutingWorkflowState): Task iggygetout_trim_fastqc.postfastqc:1:1 failed. The job was stopped before the command finished. PAPI error code 10. Message: 14: VM ggp-17100430892766313741 stopped unexpectedly.
java.lang.Exception: Task iggygetout_trim_fastqc.postfastqc:1:1 failed. The job was stopped before the command finished. PAPI error code 10. Message: 14: VM ggp-17100430892766313741 stopped unexpectedly.
at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor$.StandardException(PipelinesApiAsyncBackendJobExecutionActor.scala:73)
at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.handleFailedRunStatus$1(PipelinesApiAsyncBackendJobExecutionActor.scala:520)
at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.handleExecutionFailure(PipelinesApiAsyncBackendJobExecutionActor.scala:527)
at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.handleExecutionFailure(PipelinesApiAsyncBackendJobExecutionActor.scala:77)
at cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$handleExecutionResult$5.applyOrElse(StandardAsyncExecutionActor.scala:1019)
at cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$handleExecutionResult$5.applyOrElse(StandardAsyncExecutionActor.scala:1015)
at scala.concurrent.Future.$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:43)
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)