i am running the example workflow locally following instrctions here:
https://gatkforums.broadinstitute.org/gatk/discussion/12521/how-to-execute-workflows-from-the-gatk-workflows-git-organization
I got an error. what went wrong? Is this due to the bam file itself? thanks
szong@gphost08 gatk-workflows]$ /gsc/software/linux-x86_64/jre1.8.0_66/bin/java -jar cromwell-33.1.jar run ./seq-format-validation/validate-bam.wdl --inputs ./seq-format-validation/validate-bam.inputs.json[2018-09-24 16:53:11,97] [info] Running with database db.url = jdbc:hsqldb:mem:5a8b3c34-4e77-4260-b284-156e4ff20c55;shutdown=false;hsqldb.tx=mvcc
[2018-09-24 16:53:21,55] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-09-24 16:53:21,57] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-09-24 16:53:21,67] [info] Running with database db.url = jdbc:hsqldb:mem:3e6a191d-dc8a-4990-b523-dec612287786;shutdown=false;hsqldb.tx=mvcc
[2018-09-24 16:53:22,19] [info] Slf4jLogger started
[2018-09-24 16:53:22,61] [info] Workflow heartbeat configuration:
{
"cromwellId" : "cromid-d687857",
"heartbeatInterval" : "2 minutes",
"ttl" : "10 minutes",
"writeBatchSize" : 10000,
"writeThreshold" : 10000
}
[2018-09-24 16:53:22,68] [info] Metadata summary refreshing every 2 seconds.
[2018-09-24 16:53:22,72] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-09-24 16:53:22,72] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-09-24 16:53:22,72] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2018-09-24 16:53:24,02] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2018-09-24 16:53:24,04] [info] SingleWorkflowRunnerActor: Submitting workflow
[2018-09-24 16:53:24,12] [info] Unspecified type (Unspecified version) workflow 92883a94-765a-414d-a0aa-9fa3f5a2e6af submitted
[2018-09-24 16:53:24,19] [info] SingleWorkflowRunnerActor: Workflow submitted 92883a94-765a-414d-a0aa-9fa3f5a2e6af
[2018-09-24 16:53:24,19] [info] 1 new workflows fetched
[2018-09-24 16:53:24,19] [info] WorkflowManagerActor Starting workflow 92883a94-765a-414d-a0aa-9fa3f5a2e6af
[2018-09-24 16:53:24,20] [info] WorkflowManagerActor Successfully started WorkflowActor-92883a94-765a-414d-a0aa-9fa3f5a2e6af
[2018-09-24 16:53:24,20] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2018-09-24 16:53:24,21] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData
[2018-09-24 16:53:24,23] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-09-24 16:53:24,24] [info] Using noop to send events.
[2018-09-24 16:53:24,27] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2018-09-24 16:53:24,30] [info] MaterializeWorkflowDescriptorActor [92883a94]: Parsing workflow as WDL draft-2
[2018-09-24 16:53:25,35] [info] MaterializeWorkflowDescriptorActor [92883a94]: Call-to-Backend assignments: ValidateBamsWf.ValidateBAM -> Local
[2018-09-24 16:53:25,50] [warn] Local [92883a94]: Key/s [memory, cpu, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-09-24 16:53:31,01] [info] WorkflowExecutionActor-92883a94-765a-414d-a0aa-9fa3f5a2e6af [92883a94]: Starting ValidateBamsWf.ValidateBAM
[2018-09-24 16:53:32,48] [warn] BackgroundConfigAsyncJobExecutionActor [92883a94ValidateBamsWf.ValidateBAM:0:1]: Unrecognized runtime attribute keys: disks, cpu, memory
[2018-09-24 16:53:33,50] [info] BackgroundConfigAsyncJobExecutionActor [92883a94ValidateBamsWf.ValidateBAM:0:1]: /gatk/gatk \
ValidateSamFile \
--INPUT /cromwell-executions/ValidateBamsWf/92883a94-765a-414d-a0aa-9fa3f5a2e6af/call-ValidateBAM/shard-0/inputs/362257838/NA12878_24RG_small.hg38.bam \
--OUTPUT NA12878_24RG_small.hg38.validation_SUMMARY.txt \
--MODE SUMMARY
[2018-09-24 16:53:33,56] [info] BackgroundConfigAsyncJobExecutionActor [92883a94ValidateBamsWf.ValidateBAM:0:1]: executing: # make sure there is no preexisting Docker CID file
rm -f /projects/da_workspace/software/gatk-workflows/cromwell-executions/ValidateBamsWf/92883a94-765a-414d-a0aa-9fa3f5a2e6af/call-ValidateBAM/shard-0/execution/docker_cid
# run as in the original configuration without --rm flag (will remove later)
docker run \
--cidfile /projects/da_workspace/software/gatk-workflows/cromwell-executions/ValidateBamsWf/92883a94-765a-414d-a0aa-9fa3f5a2e6af/call-ValidateBAM/shard-0/execution/docker_cid \
-i \
\
--entrypoint /bin/bash \
-v /projects/da_workspace/software/gatk-workflows/cromwell-executions/ValidateBamsWf/92883a94-765a-414d-a0aa-9fa3f5a2e6af/call-ValidateBAM/shard-0:/cromwell-executions/ValidateBamsWf/92883a94-765a-414d-a0aa-9fa3f5a2e6af/call-ValidateBAM/shard-0 \
broadinstitute/gatk@sha256:497185dbf683c3ae5deda0c0b42e641fad04d724d0cb887dd7d601fe30b96ca2 /cromwell-executions/ValidateBamsWf/92883a94-765a-414d-a0aa-9fa3f5a2e6af/call-ValidateBAM/shard-0/execution/script
# get the return code (working even if the container was detached)
rc=$(docker wait cat /projects/da_workspace/software/gatk-workflows/cromwell-executions/ValidateBamsWf/92883a94-765a-414d-a0aa-9fa3f5a2e6af/call-ValidateBAM/shard-0/execution/docker_cid)
# remove the container after waiting
docker rm cat /projects/da_workspace/software/gatk-workflows/cromwell-executions/ValidateBamsWf/92883a94-765a-414d-a0aa-9fa3f5a2e6af/call-ValidateBAM/shard-0/execution/docker_cid
# return exit code
exit $rc
[2018-09-24 16:53:37,77] [info] BackgroundConfigAsyncJobExecutionActor [92883a94ValidateBamsWf.ValidateBAM:0:1]: job id: 123319
[2018-09-24 16:53:37,78] [info] BackgroundConfigAsyncJobExecutionActor [92883a94ValidateBamsWf.ValidateBAM:0:1]: Status change from - to Done
[2018-09-24 16:53:38,56] [error] WorkflowManagerActor Workflow 92883a94-765a-414d-a0aa-9fa3f5a2e6af failed (during ExecutingWorkflowState): Job ValidateBamsWf.ValidateBAM:0:1 exited with return code -1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /projects/da_workspace/software/gatk-workflows/cromwell-executions/ValidateBamsWf/92883a94-765a-414d-a0aa-9fa3f5a2e6af/call-ValidateBAM/shard-0/execution/stderr.
Could not retrieve content: /projects/da_workspace/software/gatk-workflows/cromwell-executions/ValidateBamsWf/92883a94-765a-414d-a0aa-9fa3f5a2e6af/call-ValidateBAM/shard-0/execution/stderr
[2018-09-24 16:53:38,56] [info] WorkflowManagerActor WorkflowActor-92883a94-765a-414d-a0aa-9fa3f5a2e6af is in a terminal state: WorkflowFailedState
[2018-09-24 16:53:45,29] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2018-09-24 16:53:47,74] [info] Workflow polling stopped
[2018-09-24 16:53:47,76] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2018-09-24 16:53:47,76] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2018-09-24 16:53:47,77] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2018-09-24 16:53:47,77] [info] Aborting all running workflows.
[2018-09-24 16:53:47,77] [info] JobExecutionTokenDispenser stopped
[2018-09-24 16:53:47,77] [info] WorkflowStoreActor stopped
[2018-09-24 16:53:47,78] [info] WorkflowLogCopyRouter stopped
[2018-09-24 16:53:47,78] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2018-09-24 16:53:47,78] [info] WorkflowManagerActor All workflows finished
[2018-09-24 16:53:47,78] [info] WorkflowManagerActor stopped
[2018-09-24 16:53:47,78] [info] Connection pools shut down
[2018-09-24 16:53:47,79] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2018-09-24 16:53:47,79] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2018-09-24 16:53:47,79] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2018-09-24 16:53:47,79] [info] SubWorkflowStoreActor stopped
[2018-09-24 16:53:47,79] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2018-09-24 16:53:47,79] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2018-09-24 16:53:47,79] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2018-09-24 16:53:47,79] [info] JobStoreActor stopped
[2018-09-24 16:53:47,79] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2018-09-24 16:53:47,79] [info] KvWriteActor Shutting down: 0 queued messages to process
[2018-09-24 16:53:47,79] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2018-09-24 16:53:47,79] [info] CallCacheWriteActor stopped
[2018-09-24 16:53:47,79] [info] DockerHashActor stopped
[2018-09-24 16:53:47,79] [info] IoProxy stopped
[2018-09-24 16:53:47,80] [info] ServiceRegistryActor stopped
[2018-09-24 16:53:47,83] [info] Database closed
[2018-09-24 16:53:47,83] [info] Stream materializer shut down
Workflow 92883a94-765a-414d-a0aa-9fa3f5a2e6af transitioned to state Failed
[2018-09-24 16:53:47,89] [info] Automatic shutdown of the async connection
[2018-09-24 16:53:47,89] [info] Gracefully shutdown sentry threads.
[2018-09-24 16:53:47,89] [info] Shutdown finished.