cromwell wdl

cromwell.log

$ time java  -jar cromwell-57.jar  run  jeter.wdl 

[2021-02-24 18:43:16,75] [info] Running with database db.url = jdbc:hsqldb:mem:43a7a2b5-d8e7-4129-a9d5-c939dbf31ddf;shutdown=false;hsqldb.tx=mvcc
[2021-02-24 18:45:41,45] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2021-02-24 18:45:42,04] [info] [RenameWorkflowOptionsInMetadata] 100%
[2021-02-24 18:45:44,94] [info] Running with database db.url = jdbc:hsqldb:mem:f57101ad-0a60-4bc1-947f-efb7610b1497;shutdown=false;hsqldb.tx=mvcc
[2021-02-24 18:45:55,25] [info] Slf4jLogger started
[2021-02-24 18:45:58,25] [info] Workflow heartbeat configuration:
{
  "cromwellId" : "cromid-3d07b24",
  "heartbeatInterval" : "2 minutes",
  "ttl" : "10 minutes",
  "failureShutdownDuration" : "5 minutes",
  "writeBatchSize" : 10000,
  "writeThreshold" : 10000
}
[2021-02-24 18:45:59,15] [info] Metadata summary refreshing every 1 second.
[2021-02-24 18:45:59,65] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2021-02-24 18:45:59,65] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2021-02-24 18:46:31,34] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2021-02-24 18:46:31,34] [warn] 'docker.hash-lookup.gcr-api-queries-per-100-seconds' is being deprecated, use 'docker.hash-lookup.gcr.throttle' instead (see reference.conf)
[2021-02-24 18:46:33,44] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2021-02-24 18:46:34,55] [info] SingleWorkflowRunnerActor: Version 57
[2021-02-24 18:46:34,84] [info] SingleWorkflowRunnerActor: Submitting workflow
[2021-02-24 18:46:37,65] [info] Unspecified type (Unspecified version) workflow 082c2158-2dd7-4570-836e-43ebcb360f0a submitted
[2021-02-24 18:46:38,54] [info] Not triggering log of token queue status. Effective log interval = None
[2021-02-24 18:46:38,54] [info] SingleWorkflowRunnerActor: Workflow submitted 082c2158-2dd7-4570-836e-43ebcb360f0a
[2021-02-24 18:46:38,85] [info] 1 new workflows fetched by cromid-3d07b24: 082c2158-2dd7-4570-836e-43ebcb360f0a
[2021-02-24 18:46:39,44] [info] WorkflowManagerActor Starting workflow 082c2158-2dd7-4570-836e-43ebcb360f0a
[2021-02-24 18:46:40,14] [info] WorkflowManagerActor Successfully started WorkflowActor-082c2158-2dd7-4570-836e-43ebcb360f0a
[2021-02-24 18:46:40,14] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2021-02-24 18:46:41,54] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2021-02-24 18:46:46,94] [info] MaterializeWorkflowDescriptorActor [082c2158]: Parsing workflow as WDL draft-2
[2021-02-24 18:47:18,75] [info] MaterializeWorkflowDescriptorActor [082c2158]: Call-to-Backend assignments: FilterVcf.MyTask -> Local
[2021-02-24 18:47:24,44] [info] WorkflowExecutionActor-082c2158-2dd7-4570-836e-43ebcb360f0a [082c2158]: Starting FilterVcf.MyTask
[2021-02-24 18:47:25,65] [info] Assigned new job execution tokens to the following groups: 082c2158: 1
[2021-02-24 18:47:29,54] [info] BackgroundConfigAsyncJobExecutionActor [082c2158FilterVcf.MyTask:NA:1]: echo "Hello world"
[2021-02-24 18:47:31,54] [info] BackgroundConfigAsyncJobExecutionActor [082c2158FilterVcf.MyTask:NA:1]: executing: /bin/bash /path/to/cromwell-executions/FilterVcf/082c2158-2dd7-4570-836e-43ebcb360f0a/call-MyTask/execution/script
[2021-02-24 18:47:35,14] [info] BackgroundConfigAsyncJobExecutionActor [082c2158FilterVcf.MyTask:NA:1]: job id: 22994
[2021-02-24 18:47:35,25] [info] BackgroundConfigAsyncJobExecutionActor [082c2158FilterVcf.MyTask:NA:1]: Status change from - to Done
[2021-02-24 18:47:37,84] [info] WorkflowExecutionActor-082c2158-2dd7-4570-836e-43ebcb360f0a [082c2158]: Workflow FilterVcf complete. Final Outputs:
{
  "FilterVcf.MyTask.out": "Hello world"
}
[2021-02-24 18:47:38,55] [info] WorkflowManagerActor WorkflowActor-082c2158-2dd7-4570-836e-43ebcb360f0a is in a terminal state: WorkflowSucceededState
[2021-02-24 18:47:42,34] [info] SingleWorkflowRunnerActor workflow finished with status 'Succeeded'.
{
  "outputs": {
    "FilterVcf.MyTask.out": "Hello world"
  },
  "id": "082c2158-2dd7-4570-836e-43ebcb360f0a"
}
[2021-02-24 18:47:45,55] [info] Workflow polling stopped
[2021-02-24 18:47:45,84] [info] 0 workflows released by cromid-3d07b24
[2021-02-24 18:47:45,85] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2021-02-24 18:47:45,95] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2021-02-24 18:47:46,04] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2021-02-24 18:47:46,04] [info] JobExecutionTokenDispenser stopped
[2021-02-24 18:47:46,14] [info] Aborting all running workflows.
[2021-02-24 18:47:46,14] [info] WorkflowStoreActor stopped
[2021-02-24 18:47:46,15] [info] WorkflowLogCopyRouter stopped
[2021-02-24 18:47:46,15] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2021-02-24 18:47:46,15] [info] WorkflowManagerActor All workflows finished
[2021-02-24 18:47:46,15] [info] WorkflowManagerActor stopped
[2021-02-24 18:47:49,84] [warn] SingleWorkflowRunnerActor: received unexpected message: QueueWeight(0) of type cromwell.core.actor.BatchActor.QueueWeight in state RequestingOutputs
[2021-02-24 18:47:50,14] [info] Connection pools shut down
[2021-02-24 18:47:50,15] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2021-02-24 18:47:50,15] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2021-02-24 18:47:50,15] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2021-02-24 18:47:50,15] [info] SubWorkflowStoreActor stopped
[2021-02-24 18:47:50,15] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2021-02-24 18:47:50,15] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2021-02-24 18:47:50,15] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2021-02-24 18:47:50,15] [info] JobStoreActor stopped
[2021-02-24 18:47:50,15] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2021-02-24 18:47:50,15] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2021-02-24 18:47:50,15] [info] KvWriteActor Shutting down: 0 queued messages to process
[2021-02-24 18:47:50,24] [info] IoProxy stopped
[2021-02-24 18:47:50,24] [info] CallCacheWriteActor stopped
[2021-02-24 18:47:50,24] [info] ServiceRegistryActor stopped
[2021-02-24 18:47:50,44] [info] DockerHashActor stopped
[2021-02-24 18:47:51,15] [info] Database closed
[2021-02-24 18:47:51,24] [info] Stream materializer shut down
[2021-02-24 18:47:51,24] [info] WDL HTTP import resolver closed

real	5m4.000s
user	1m47.615s
sys	0m6.705s

jeter.wdl

workflow FilterVcf {
    call MyTask
    }


task MyTask {
   command {
	echo "Hello world"
	}
    output {
	String out = read_string(stdout())
	}
    }