I am testing a soapfuse docker image locally and failed:
WDL file,
workflow soapfuseref {
call soapfuseref
}
task soapfuseref {
String genome
File cytoB
File HGNC
File fa
File gtf
command {
./constructBase.sh ${genome} ${cytoB} ${HGNC} ${fa} ${gtf}
}
runtime { docker: "avkitex/soapfuse-ref" }
}
json file,
{
"soapfuseref.soapfuseref.genome": "/home/bianxi/hg19-GRCh37/hg19GRCh37",
"soapfuseref.soapfuseref.cytoB": "/home/bianxi/hg19-GRCh37/cytoBand.txt",
"soapfuseref.soapfuseref.HGNC": "/home/bianxi/hg19-GRCh37/hgnc_complete_set.txt",
"soapfuseref.soapfuseref.fa": "/home/bianxi/hg19-GRCh37/hg19.fa",
"soapfuseref.soapfuseref.gtf": "/home/bianxi/hg19-GRCh37/Homo_sapiens.gtf"
}
run with,
java -jar ~/Workshop_Materials/bin/cromwell-0.19.jar run ~/firecloud/soapfuse-ref.wdl ~/firecloud/soapfuse-ref_input.json
got the following error, it's overwhelming for me, could someone pin point what was exactly wrong?
[2016-06-29 12:38:58,362] [info] Slf4jLogger started
[2016-06-29 12:38:58,380] [info] RUN sub-command
[2016-06-29 12:38:58,380] [info] WDL file: /home/bianxi/firecloud/soapfuse-ref.wdl
[2016-06-29 12:38:58,380] [info] Inputs: /home/bianxi/firecloud/soapfuse-ref_input.json
[2016-06-29 12:38:58,401] [info] SingleWorkflowRunnerActor: launching workflow
[2016-06-29 12:38:58,784] [info] Running with database db.url = jdbc:hsqldb:mem:feaf3945-14ab-421f-9825-6855bae16c69;shutdown=false;hsqldb.tx=mvcc
[2016-06-29 12:39:01,366] [info] WorkflowManagerActor submitWorkflow input id = None, effective id = 6d073f5d-f2b1-4594-8ecc-98b201965ec9
[2016-06-29 12:39:01,385] [info] WorkflowManagerActor Found no workflows to restart.
Jun 29, 2016 12:39:01 PM com.google.api.client.googleapis.services.AbstractGoogleClient
WARNING: Application name is not set. Call Builder#setApplicationName.
[2016-06-29 12:39:01,910] [info] Updating WorkflowManager state. New Data: (6d073f5d-f2b1-4594-8ecc-98b201965ec9,Actor[akka://cromwell-system/user/WorkflowManagerActor/WorkflowActor-6d073f5d-f2b1-4594-8ecc-98b201965ec9#601584227])
[2016-06-29 12:39:01,925] [info] WorkflowActor [6d073f5d]: Start(Some(Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor#644177576])) message received
[2016-06-29 12:39:02,01] [info] SingleWorkflowRunnerActor: workflow ID 6d073f5d-f2b1-4594-8ecc-98b201965ec9
[2016-06-29 12:39:02,04] [info] WorkflowActor [6d073f5d]: ExecutionStoreCreated(Start(Some(Actor[akka://cromwell-system/user/SingleWorkflowRunnerActor#644177576]))) message received
[2016-06-29 12:39:02,11] [info] WorkflowActor [6d073f5d]: Beginning transition from Submitted to Running.
[2016-06-29 12:39:02,16] [info] WorkflowActor [6d073f5d]: transitioning from Submitted to Running.
[2016-06-29 12:39:02,17] [info] WorkflowActor [6d073f5d]: starting calls: soapfuseref.soapfuseref
[2016-06-29 12:39:02,20] [info] WorkflowActor [6d073f5d]: persisting status of soapfuseref to Starting.
[2016-06-29 12:39:02,27] [warn] Found unsupported keys for backend 'LOCAL': bootDiskSizeGb, cpu, disks, memory, preemptible, zones
[2016-06-29 12:39:02,80] [info] WorkflowActor [6d073f5d]: inputs for call 'soapfuseref':
HGNC -> WdlSingleFile(/home/bianxi/hg19-GRCh37/hgnc_complete_set.txt)
gtf -> WdlSingleFile(/home/bianxi/hg19-GRCh37/Homo_sapiens.gtf)
cytoB -> WdlSingleFile(/home/bianxi/hg19-GRCh37/cytoBand.txt)
genome -> WdlString(/home/bianxi/hg19-GRCh37/hg19GRCh37)
fa -> WdlSingleFile(/home/bianxi/hg19-GRCh37/hg19.fa)
[2016-06-29 12:39:02,82] [info] WorkflowActor [6d073f5d]: created call actor for soapfuseref.
[2016-06-29 12:39:02,91] [warn] Found unsupported keys for backend 'LOCAL': bootDiskSizeGb, cpu, disks, memory, preemptible, zones
[2016-06-29 12:39:02,100] [info] WorkflowActor [6d073f5d]: persisting status of soapfuseref to Running.
[2016-06-29 12:39:02,116] [info] LocalBackend [6d073f5d:soapfuseref]: ./constructBase.sh /home/bianxi/hg19-GRCh37/hg19GRCh37 /root/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/home/bianxi/hg19-GRCh37/cytoBand.txt /root/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/home/bianxi/hg19-GRCh37/hgnc_complete_set.txt /root/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/home/bianxi/hg19-GRCh37/hg19.fa /root/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/home/bianxi/hg19-GRCh37/Homo_sapiens.gtf
[2016-06-29 12:39:06,375] [error] LocalBackend [6d073f5d:soapfuseref]: Non-zero return code: 1
[2016-06-29 12:39:06,375] [error] LocalBackend [6d073f5d:soapfuseref]: Standard error was:
Contents of cromwell-executions/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/stderr were empty.
[2016-06-29 12:39:06,386] [error] CallActor [6d073f5d:soapfuseref]: Failing call: Call soapfuseref.soapfuseref, Workflow 6d073f5d-f2b1-4594-8ecc-98b201965ec9: return code was (none)
Full command was: "/bin/bash" "-c" "cat cromwell-executions/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/script | docker run --rm -v /home/bianxi/firecloud/cromwell-executions/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref:/root/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref -i avkitex/soapfuse-ref /bin/bash <&0"
Contents of cromwell-executions/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/stderr were empty.
java.lang.Throwable: Call soapfuseref.soapfuseref, Workflow 6d073f5d-f2b1-4594-8ecc-98b201965ec9: return code was (none)
Full command was: "/bin/bash" "-c" "cat cromwell-executions/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/script | docker run --rm -v /home/bianxi/firecloud/cromwell-executions/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref:/root/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref -i avkitex/soapfuse-ref /bin/bash <&0"
Contents of cromwell-executions/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/stderr were empty.
at cromwell.engine.backend.local.LocalBackend.cromwell$engine$backend$local$LocalBackend$$runSubprocess(LocalBackend.scala:221)
at cromwell.engine.backend.local.LocalBackend$$anonfun$execute$1.apply(LocalBackend.scala:119)
at cromwell.engine.backend.local.LocalBackend$$anonfun$execute$1.apply(LocalBackend.scala:113)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: java.lang.Exception: Unexpected process exit code: 1
at cromwell.engine.backend.local.LocalBackend$$anonfun$3.apply$mcI$sp(LocalBackend.scala:190)
at cromwell.engine.backend.local.LocalBackend$$anonfun$3.apply(LocalBackend.scala:183)
at cromwell.engine.backend.local.LocalBackend$$anonfun$3.apply(LocalBackend.scala:183)
at scala.util.Try$.apply(Try.scala:192)
at cromwell.engine.backend.local.LocalBackend.cromwell$engine$backend$local$LocalBackend$$runSubprocess(LocalBackend.scala:182)
... 10 common frames omitted
[2016-06-29 12:39:06,386] [info] WorkflowActor [6d073f5d]: persisting status of soapfuseref to Failed.
[2016-06-29 12:39:06,387] [error] WorkflowActor [6d073f5d]: Call soapfuseref.soapfuseref, Workflow 6d073f5d-f2b1-4594-8ecc-98b201965ec9: return code was (none)
Full command was: "/bin/bash" "-c" "cat cromwell-executions/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/script | docker run --rm -v /home/bianxi/firecloud/cromwell-executions/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref:/root/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref -i avkitex/soapfuse-ref /bin/bash <&0"
Contents of cromwell-executions/soapfuseref/6d073f5d-f2b1-4594-8ecc-98b201965ec9/call-soapfuseref/stderr were empty.
[2016-06-29 12:39:06,422] [info] WorkflowActor [6d073f5d]: Beginning transition from Running to Failed.
[2016-06-29 12:39:06,431] [info] WorkflowActor [6d073f5d]: transitioning from Running to Failed.
[2016-06-29 12:39:06,432] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2016-06-29 12:39:06,433] [error] Workflow 6d073f5d-f2b1-4594-8ecc-98b201965ec9 transitioned to state Failed
java.lang.Throwable: Workflow 6d073f5d-f2b1-4594-8ecc-98b201965ec9 transitioned to state Failed
at cromwell.engine.workflow.SingleWorkflowRunnerActor$RunnerData.addFailure(SingleWorkflowRunnerActor.scala:42)
at cromwell.engine.workflow.SingleWorkflowRunnerActor$$anonfun$2.applyOrElse(SingleWorkflowRunnerActor.scala:89)
at cromwell.engine.workflow.SingleWorkflowRunnerActor$$anonfun$2.applyOrElse(SingleWorkflowRunnerActor.scala:80)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
at akka.actor.FSM$class.processEvent(FSM.scala:604)
at cromwell.engine.workflow.SingleWorkflowRunnerActor.akka$actor$LoggingFSM$$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 6d073f5d-f2b1-4594-8ecc-98b201965ec9 transitioned to state Failed