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Cromwell: dead letters encountered

I am using Cromwell to run haplotypecaller-gvcf-gatk4.wdl. But it doesn't wok. Also docker is not invoked.

[2018-03-24 15:55:59,90] [info] Running with database db.url = jdbc:hsqldb:mem:0f146367-d1ec-42c5-b5a2-c495444c78a2;shutdown=false;hsqldb.tx=mvcc
[2018-03-24 15:56:06,05] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-03-24 15:56:06,07] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-03-24 15:56:06,16] [info] Running with database db.url = jdbc:hsqldb:mem:be02d29c-fa92-44ad-aaa6-5a1630cad08d;shutdown=false;hsqldb.tx=mvcc
[2018-03-24 15:56:06,54] [info] Slf4jLogger started
[2018-03-24 15:56:06,74] [info] Metadata summary refreshing every 2 seconds.
[2018-03-24 15:56:06,78] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-03-24 15:56:06,78] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-03-24 15:56:06,79] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2018-03-24 15:56:07,48] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2018-03-24 15:56:07,50] [info] SingleWorkflowRunnerActor: Submitting workflow
[2018-03-24 15:56:07,54] [info] WDL (Unspecified version) workflow 5382cf0c-16ae-44dc-a817-047c34161ae2 submitted
[2018-03-24 15:56:07,54] [info] SingleWorkflowRunnerActor: Workflow submitted 5382cf0c-16ae-44dc-a817-047c34161ae2
[2018-03-24 15:56:07,54] [info] 1 new workflows fetched
[2018-03-24 15:56:07,54] [info] WorkflowManagerActor Starting workflow 5382cf0c-16ae-44dc-a817-047c34161ae2
[2018-03-24 15:56:07,55] [info] WorkflowManagerActor Successfully started WorkflowActor-5382cf0c-16ae-44dc-a817-047c34161ae2
[2018-03-24 15:56:07,55] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2018-03-24 15:56:08,57] [info] MaterializeWorkflowDescriptorActor [5382cf0c]: Call-to-Backend assignments: HaplotypeCallerGvcf_GATK4.HaplotypeCaller -> Local, HaplotypeCallerGvcf_GATK4.MergeGVCFs -> Local
[2018-03-24 15:56:08,67] [warn] Local [5382cf0c]: Key/s [memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-03-24 15:56:08,67] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-03-24 15:56:08,68] [info] Using noop to send events.
[2018-03-24 15:56:08,69] [warn] Local [5382cf0c]: Key/s [memory, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-03-24 15:56:14,59] [info] Message [cromwell.docker.DockerHashActor$DockerHashSuccessResponse] from Actor[akka://cromwell-system/user/HealthMonitorDockerHashActor#1021524121] to Actor[akka://cromwell-system/deadLetters] was not delivered. [1] dead letters encountered. This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.
[2018-03-24 15:56:47,76] [info] Message [cromwell.docker.DockerHashActor$DockerHashSuccessResponse] from Actor[akka://cromwell-system/user/HealthMonitorDockerHashActor#1021524121] to Actor[akka://cromwell-system/deadLetters] was not delivered. [2] dead letters encountered. This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.
[2018-03-24 16:02:27,07] [info] Message [cromwell.docker.DockerHashActor$DockerHashSuccessResponse] from Actor[akka://cromwell-system/user/HealthMonitorDockerHashActor#1021524121] to Actor[akka://cromwell-system/deadLetters] was not delivered. [3] dead letters encountered. This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.
[2018-03-24 16:03:02,06] [info] Message [cromwell.docker.DockerHashActor$DockerHashSuccessResponse] from Actor[akka://cromwell-system/user/HealthMonitorDockerHashActor#1021524121] to Actor[akka://cromwell-system/deadLetters] was not delivered. [4] dead letters encountered. This logging can be turned off or adjusted with configuration settings 'akka.log-dead-letters' and 'akka.log-dead-letters-during-shutdown'.

Answers

  • ThibThib CambridgeMember, Broadie, Dev

    Hi !
    Is this the end of the Cromwell log or is there more ? This message looks scary but should not actually be the cause of a failing workflow.

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