Hi
Developing a module for firecloud and testing the docker for the module, I am seeing many errors from cromwell and I have no idea how to interpret the errors. Is there a docker / cromwell expert that I could contact for help?
Here are the errors:
$ java -jar cromwell-0.17.jar run FFPE-filter.wdl test.input.json
[2016-02-19 16:18:48,707] [info] RUN sub-command
[2016-02-19 16:18:48,715] [info] WDL file: FFPE-filter.wdl
[2016-02-19 16:18:48,716] [info] Inputs: test.input.json
[2016-02-19 16:18:48,900] [info] Slf4jLogger started
[2016-02-19 16:18:48,932] [info] SingleWorkflowRunnerActor: launching workflow
[2016-02-19 16:18:49,519] [info] Running with database db.url = jdbc:hsqldb:mem:51fc8b70-f6b2-4e7d-a7c9-1f45ccb04444;shutdown=false;hsqldb.tx=mvcc
[2016-02-19 16:18:49,962] [info] WorkflowManagerActor submitWorkflow input id = None, effective id = fa92e815-7655-47f1-b62b-8c65f240dc70
[2016-02-19 16:18:49,983] [info] WorkflowManagerActor Found no workflows to restart.
[2016-02-19 16:18:50,334] [warn] Found unsupported keys for backend 'LOCAL': defaultDisks, memory
[2016-02-19 16:18:50,398] [info] WorkflowActor [fa92e815]: Start message received
[2016-02-19 16:18:50,512] [info] WorkflowActor [fa92e815]: ExecutionStoreCreated(Start) message received
[2016-02-19 16:18:50,513] [info] SingleWorkflowRunnerActor: workflow ID fa92e815-7655-47f1-b62b-8c65f240dc70
[2016-02-19 16:18:50,521] [info] WorkflowActor [fa92e815]: Beginning transition from Submitted to Running.
[2016-02-19 16:18:50,522] [warn] SingleWorkflowRunnerActor: received unexpected message: CurrentState(Actor[akka://cromwell-system/user/WorkflowManagerActor/WorkflowActor-fa92e815-7655-47f1-b62b-8c65f240dc70#-1755188897],Submitted)
[2016-02-19 16:18:50,522] [info] WorkflowActor [fa92e815]: transitioning from Submitted to Running.
[2016-02-19 16:18:50,523] [info] SingleWorkflowRunnerActor: transitioning to Running
[2016-02-19 16:18:50,525] [info] WorkflowActor [fa92e815]: starting calls: FFPE_filter.FFPE_filter_Task
[2016-02-19 16:18:50,526] [info] WorkflowActor [fa92e815]: persisting status of FFPE_filter_Task to Starting.
[2016-02-19 16:18:50,541] [warn] Found unsupported keys for backend 'LOCAL': defaultDisks, memory
[2016-02-19 16:18:50,713] [info] WorkflowActor [fa92e815]: inputs for call 'FFPE_filter_Task':
OUT -> WdlString(.)
MAF -> WdlSingleFile(/Users/stewart/Projects/seq/TCGA-BL-A0C8-01B-04D-A271-08.1p.maf)
REFERENCE -> WdlSingleFile(/Users/stewart/Projects/seq/references/Homo_sapiens_assembly19/v1/chr1p.fasta)
DBSNP -> WdlSingleFile(/Users/stewart/Projects/seq/dbsnp_134_b37.leftAligned.1p.vcf)
ALIQUOT -> WdlString(TCGA-BL-A0C8-01B-04D-A271-08)
BAM -> WdlSingleFile(/Users/stewart/Projects/seq/TCGA-BL-A0C8-01B-04D-A271-08.1p.bam)
[2016-02-19 16:18:50,715] [info] WorkflowActor [fa92e815]: created call actor for FFPE_filter_Task.
[2016-02-19 16:18:50,720] [info] WorkflowActor [fa92e815]: persisting status of FFPE_filter_Task to Running.
[2016-02-19 16:18:50,726] [warn] Found unsupported keys for backend 'LOCAL': defaultDisks, memory
[2016-02-19 16:18:50,784] [info] LocalBackend [fa92e815:FFPE_filter_Task]: # FFPE filter
source run_FFPE_filter.sh TCGA-BL-A0C8-01B-04D-A271-08 /root/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task/Users/stewart/Projects/seq/TCGA-BL-A0C8-01B-04D-A271-08.1p.bam /root/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task/Users/stewart/Projects/seq/TCGA-BL-A0C8-01B-04D-A271-08.1p.maf /root/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task/Users/stewart/Projects/seq/references/Homo_sapiens_assembly19/v1/chr1p.fasta /root/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task/Users/stewart/Projects/seq/dbsnp_134_b37.leftAligned.1p.vcf . ;
[2016-02-19 16:18:51,874] [error] LocalBackend [fa92e815:FFPE_filter_Task]: Non-zero return code: 1
[2016-02-19 16:18:51,874] [error] LocalBackend [fa92e815:FFPE_filter_Task]: Standard error was:
Contents of cromwell-executions/FFPE_filter/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task/stderr:
Unable to find image '18ce069d2eb9:latest' locally
Pulling repository docker.io/library/18ce069d2eb9
Error: image library/18ce069d2eb9:latest not found
[2016-02-19 16:18:51,887] [error] CallActor [fa92e815:FFPE_filter_Task]: Failing call: Call FFPE_filter.FFPE_filter_Task, Workflow fa92e815-7655-47f1-b62b-8c65f240dc70: return code was (none)
Full command was: "/bin/bash" "-c" "cat cromwell-executions/FFPE_filter/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task/script | docker run --rm -v /Users/stewart/Projects/Docker/cromwell-executions/FFPE_filter/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task:/root/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task -i 18ce069d2eb9 /bin/bash <&0"
Contents of cromwell-executions/FFPE_filter/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task/stderr:
Unable to find image '18ce069d2eb9:latest' locally
Pulling repository docker.io/library/18ce069d2eb9
Error: image library/18ce069d2eb9:latest not found
java.lang.Throwable: Call FFPE_filter.FFPE_filter_Task, Workflow fa92e815-7655-47f1-b62b-8c65f240dc70: return code was (none)
Full command was: "/bin/bash" "-c" "cat cromwell-executions/FFPE_filter/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task/script | docker run --rm -v /Users/stewart/Projects/Docker/cromwell-executions/FFPE_filter/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task:/root/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task -i 18ce069d2eb9 /bin/bash <&0"
Contents of cromwell-executions/FFPE_filter/fa92e815-7655-47f1-b62b-8c65f240dc70/call-FFPE_filter_Task/stderr:
Unable to find image '18ce069d2eb9:latest' locally
Pulling repository docker.io/library/18ce069d2eb9
Error: image library/18ce069d2eb9:latest not found
at cromwell.engine.backend.local.LocalBackend.cromwell$engine$backend$local$LocalBackend$$runSubprocess(LocalBackend.scala:246)
at cromwell.engine.backend.local.LocalBackend$$anonfun$execute$1.apply(LocalBackend.scala:144)
at cromwell.engine.backend.local.LocalBackend$$anonfun$execute$1.apply(LocalBackend.scala:138)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: java.lang.Exception: Unexpected process exit code: 1
at cromwell.engine.backend.local.LocalBackend$$anonfun$3.apply$mcI$sp(LocalBackend.scala:215)
at cromwell.engine.backend.local.LocalBackend$$anonfun$3.apply(LocalBackend.scala:208)
at cromwell.engine.backend.local.LocalBackend$$anonfun$3.apply(LocalBackend.scala:208)
at scala.util.Try$.apply(Try.scala:192)
at cromwell.engine.backend.local.LocalBackend.cromwell$engine$backend$local$LocalBackend$$runSubprocess(LocalBackend.scala:207)
... 10 common frames omitted
[2016-02-19 16:18:51,889] [info] WorkflowActor [fa92e815]: persisting status of FFPE_filter_Task to Failed.
[2016-02-19 16:18:51,890] [info] WorkflowActor [fa92e815]: Beginning transition from Running to Failed.
[2016-02-19 16:18:51,901] [info] WorkflowActor [fa92e815]: transitioning from Running to Failed.
[2016-02-19 16:18:51,902] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2016-02-19 16:18:51,903] [error] Workflow fa92e815-7655-47f1-b62b-8c65f240dc70 transitioned to state Failed
java.lang.Throwable: Workflow fa92e815-7655-47f1-b62b-8c65f240dc70 transitioned to state Failed
at cromwell.engine.workflow.SingleWorkflowRunnerActor$RunnerData.addFailure(SingleWorkflowRunnerActor.scala:42)
at cromwell.engine.workflow.SingleWorkflowRunnerActor$$anonfun$2.applyOrElse(SingleWorkflowRunnerActor.scala:100)
at cromwell.engine.workflow.SingleWorkflowRunnerActor$$anonfun$2.applyOrElse(SingleWorkflowRunnerActor.scala:78)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
at akka.actor.FSM$class.processEvent(FSM.scala:604)
at cromwell.engine.workflow.SingleWorkflowRunnerActor.akka$actor$LoggingFSM$$super$processEvent(SingleWorkflowRunnerActor.scala:53)
at akka.actor.LoggingFSM$class.processEvent(FSM.scala:734)
at cromwell.engine.workflow.SingleWorkflowRunnerActor.processEvent(SingleWorkflowRunnerActor.scala:53)
at akka.actor.FSM$class.akka$actor$FSM$$processMsg(FSM.scala:598)
at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:592)
at akka.actor.Actor$class.aroundReceive(Actor.scala:467)
at cromwell.engine.workflow.SingleWorkflowRunnerActor.aroundReceive(SingleWorkflowRunnerActor.scala:53)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516)
at akka.actor.ActorCell.invoke(ActorCell.scala:487)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238)
at akka.dispatch.Mailbox.run(Mailbox.scala:220)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Workflow fa92e815-7655-47f1-b62b-8c65f240dc70 transitioned to state Failed