tmp
-
[INFO] [12/18/2025 07:05:32.113] [cromwell-system-akka.dispatchers.backend-dispatcher-1244] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-9c9d7421-4218-4a3f-9f46-87faa5edc47e/WorkflowExecutionActor-9c9d7421-4218-4a3f-9f46-87faa5edc47e/9c9d7421-4218-4a3f-9f46-87faa5edc47e-EngineJobExecutionActor-monoMeth.jsonFile:NA:1/9c9d7421-4218-4a3f-9f46-87faa5edc47e-BackendJobExecutionActor-monoMeth.jsonFile:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(9c9d7421)monoMeth.jsonFile:NA:1]: Job task-9a3b0fd9 is complete
[INFO] [12/18/2025 07:05:32.113] [cromwell-system-akka.dispatchers.backend-dispatcher-1255] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-9c9d7421-4218-4a3f-9f46-87faa5edc47e/WorkflowExecutionActor-9c9d7421-4218-4a3f-9f46-87faa5edc47e/9c9d7421-4218-4a3f-9f46-87faa5edc47e-EngineJobExecutionActor-monoMeth.jsonFile:NA:1/9c9d7421-4218-4a3f-9f46-87faa5edc47e-BackendJobExecutionActor-monoMeth.jsonFile:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(9c9d7421)monoMeth.jsonFile:NA:1]: Status change from Running to Complete -
[INFO] [12/18/2025 07:26:16.905] [cromwell-system-akka.dispatchers.api-dispatcher-1503] [akka://cromwell-system/user/cromwell-service/WorkflowStoreActor/WorkflowStoreSubmitActor] Unspecified type (Unspecified version) workflow b3c8ad44-dc3b-4e87-9fe9-97c0db47031b submitted
[INFO] [12/18/2025 07:26:31.291] [cromwell-system-akka.dispatchers.engine-dispatcher-68] [akka://cromwell-system/user/cromwell-service/WorkflowStoreActor/WorkflowStoreEngineActor] 1 new workflows fetched by cromid-247fb6c: b3c8ad44-dc3b-4e87-9fe9-97c0db47031b
[INFO] [12/18/2025 07:26:31.291] [cromwell-system-akka.dispatchers.engine-dispatcher-68] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor] WorkflowManagerActor: Starting workflow UUID(b3c8ad44-dc3b-4e87-9fe9-97c0db47031b)
[INFO] [12/18/2025 07:26:31.291] [cromwell-system-akka.dispatchers.engine-dispatcher-68] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor] WorkflowManagerActor: Successfully started WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b
[INFO] [12/18/2025 07:26:31.291] [cromwell-system-akka.dispatchers.engine-dispatcher-68] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor] Retrieved 1 workflows from the WorkflowStoreActor
[INFO] [12/18/2025 07:26:31.293] [cromwell-system-akka.dispatchers.engine-dispatcher-74] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/MaterializeWorkflowDescriptorActor] MaterializeWorkflowDescriptorActor [UUID(b3c8ad44)]: Parsing workflow as WDL draft-2
[INFO] [12/18/2025 07:26:31.298] [cromwell-system-akka.dispatchers.engine-dispatcher-74] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/MaterializeWorkflowDescriptorActor] MaterializeWorkflowDescriptorActor [UUID(b3c8ad44)]: Call-to-Backend assignments: meta_workflow.Identify_analy -> TESK
[INFO] [12/18/2025 07:26:33.508] [cromwell-system-akka.dispatchers.engine-dispatcher-74] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b] WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b [UUID(b3c8ad44)]: Starting meta_workflow.Identify_analy
[INFO] [12/18/2025 07:26:41.267] [cromwell-system-akka.dispatchers.engine-dispatcher-55] [akka://cromwell-system/user/cromwell-service/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: b3c8ad44: 1
[WARN] [12/18/2025 07:26:41.289] [cromwell-system-akka.dispatchers.engine-dispatcher-66] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/BackendPreparationActor_for_b3c8ad44:meta_workflow.Identify_analy
1] BackendPreparationActor_for_b3c8ad44:meta_workflow.Identify_analy1 [UUID(b3c8ad44)]: Docker lookup failed
java.lang.Exception: Failed to get docker hash for dockerhub.genostack.com:8090/library/ubuntu:18.04 Error running: docker images --digests --format {{printf "%s\t%s\t%s" .Repository .Tag .Digest}}
Exit code: 1
Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?at cromwell.engine.workflow.WorkflowDockerLookupActor.cromwell$engine$workflow$WorkflowDockerLookupActor$$handleLookupFailure(WorkflowDockerLookupActor.scala:279) at cromwell.engine.workflow.WorkflowDockerLookupActor$$anonfun$3.applyOrElse(WorkflowDockerLookupActor.scala:93) at cromwell.engine.workflow.WorkflowDockerLookupActor$$anonfun$3.applyOrElse(WorkflowDockerLookupActor.scala:78) at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:35) at akka.actor.FSM.processEvent(FSM.scala:707) at akka.actor.FSM.processEvent$(FSM.scala:704) at cromwell.engine.workflow.WorkflowDockerLookupActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowDockerLookupActor.scala:45) at akka.actor.LoggingFSM.processEvent(FSM.scala:847) at akka.actor.LoggingFSM.processEvent$(FSM.scala:829) at cromwell.engine.workflow.WorkflowDockerLookupActor.processEvent(WorkflowDockerLookupActor.scala:45) at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:701) at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:695) at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:35) at cromwell.docker.DockerClientHelper$$anonfun$dockerResponseReceive$1.applyOrElse(DockerClientHelper.scala:16) at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:269) at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:270) at akka.actor.Actor.aroundReceive(Actor.scala:539) at akka.actor.Actor.aroundReceive$(Actor.scala:537) at cromwell.engine.workflow.WorkflowDockerLookupActor.aroundReceive(WorkflowDockerLookupActor.scala:45) at akka.actor.ActorCell.receiveMessage(ActorCell.scala:614) at akka.actor.ActorCell.invoke(ActorCell.scala:583) at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:268) at akka.dispatch.Mailbox.run(Mailbox.scala:229) at akka.dispatch.Mailbox.exec(Mailbox.scala:241) at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)[INFO] [12/18/2025 07:26:41.631] [cromwell-system-akka.dispatchers.backend-dispatcher-1467] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]:
echo 'DATABASE' > result.txt
[INFO] [12/18/2025 07:26:41.632] [cromwell-system-akka.dispatchers.backend-dispatcher-1467] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: Calculated TES outputs (found 5):
Output(Some(rc),Some(meta_workflow.Identify_analy.rc),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/rc),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/rc,Some(FILE))
Output(Some(stdout),Some(meta_workflow.Identify_analy.stdout),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/stdout),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/stdout,Some(FILE))
Output(Some(stderr),Some(meta_workflow.Identify_analy.stderr),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/stderr),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/stderr,Some(FILE))
Output(Some(commandScript),Some(meta_workflow.Identify_analy.commandScript),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/script),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/script,Some(FILE))
Output(Some(meta_workflow.Identify_analy.output.0),Some(meta_workflow.Identify_analy.output.0),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/result.txt),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/result.txt,Some(FILE))[INFO] [12/18/2025 07:26:41.632] [cromwell-system-akka.dispatchers.backend-dispatcher-1467] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: Calculated TES inputs (found 1):
cromwell.backend.impl.tes.Input(Some(commandScript),Some(meta_workflow.Identify_analy.commandScript),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/script),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/script,Some(FILE),None)[INFO] [12/18/2025 07:26:41.632] [cromwell-system-akka.dispatchers.backend-dispatcher-1467] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]:
echo 'DATABASE' > result.txt
[INFO] [12/18/2025 07:26:46.175] [cromwell-system-akka.dispatchers.backend-dispatcher-1467] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: job id: task-710bdfb8
[INFO] [12/18/2025 07:26:47.921] [cromwell-system-akka.dispatchers.backend-dispatcher-1436] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: Status change from - to Running
[INFO] [12/18/2025 07:32:14.919] [cromwell-system-akka.dispatchers.backend-dispatcher-1436] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: Job task-710bdfb8 is complete
[INFO] [12/18/2025 07:32:14.919] [cromwell-system-akka.dispatchers.backend-dispatcher-1436] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: Status change from Running to Complete
[INFO] [12/18/2025 07:32:16.299] [cromwell-system-akka.dispatchers.engine-dispatcher-47] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b] WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b [UUID(b3c8ad44)]: Workflow meta_workflow complete. Final Outputs:
{
"meta_workflow.Identify_analy.out": "/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/result.txt"
}
[INFO] [12/18/2025 07:32:21.193] [cromwell-system-akka.dispatchers.engine-dispatcher-82] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor] WorkflowManagerActor: Workflow actor for b3c8ad44-dc3b-4e87-9fe9-97c0db47031b completed with status 'Succeeded'. The workflow will be removed from the workflow store. -
[INFO] [12/18/2025 07:26:16.905] [cromwell-system-akka.dispatchers.api-dispatcher-1503] [akka://cromwell-system/user/cromwell-service/WorkflowStoreActor/WorkflowStoreSubmitActor] Unspecified type (Unspecified version) workflow b3c8ad44-dc3b-4e87-9fe9-97c0db47031b submitted
[INFO] [12/18/2025 07:26:31.291] [cromwell-system-akka.dispatchers.engine-dispatcher-68] [akka://cromwell-system/user/cromwell-service/WorkflowStoreActor/WorkflowStoreEngineActor] 1 new workflows fetched by cromid-247fb6c: b3c8ad44-dc3b-4e87-9fe9-97c0db47031b
[INFO] [12/18/2025 07:26:31.291] [cromwell-system-akka.dispatchers.engine-dispatcher-68] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor] WorkflowManagerActor: Starting workflow UUID(b3c8ad44-dc3b-4e87-9fe9-97c0db47031b)
[INFO] [12/18/2025 07:26:31.291] [cromwell-system-akka.dispatchers.engine-dispatcher-68] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor] WorkflowManagerActor: Successfully started WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b
[INFO] [12/18/2025 07:26:31.291] [cromwell-system-akka.dispatchers.engine-dispatcher-68] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor] Retrieved 1 workflows from the WorkflowStoreActor
[INFO] [12/18/2025 07:26:31.293] [cromwell-system-akka.dispatchers.engine-dispatcher-74] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/MaterializeWorkflowDescriptorActor] MaterializeWorkflowDescriptorActor [UUID(b3c8ad44)]: Parsing workflow as WDL draft-2
[INFO] [12/18/2025 07:26:31.298] [cromwell-system-akka.dispatchers.engine-dispatcher-74] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/MaterializeWorkflowDescriptorActor] MaterializeWorkflowDescriptorActor [UUID(b3c8ad44)]: Call-to-Backend assignments: meta_workflow.Identify_analy -> TESK
[INFO] [12/18/2025 07:26:33.508] [cromwell-system-akka.dispatchers.engine-dispatcher-74] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b] WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b [UUID(b3c8ad44)]: Starting meta_workflow.Identify_analy
[INFO] [12/18/2025 07:26:41.267] [cromwell-system-akka.dispatchers.engine-dispatcher-55] [akka://cromwell-system/user/cromwell-service/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: b3c8ad44: 1
[WARN] [12/18/2025 07:26:41.289] [cromwell-system-akka.dispatchers.engine-dispatcher-66] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/BackendPreparationActor_for_b3c8ad44:meta_workflow.Identify_analy1] BackendPreparationActor_for_b3c8ad44:meta_workflow.Identify_analy1 [UUID(b3c8ad44)]: Docker lookup failed
java.lang.Exception: Failed to get docker hash for dockerhub.genostack.com:8090/library/ubuntu:18.04 Error running: docker images --digests --format {{printf "%s\t%s\t%s" .Repository .Tag .Digest}}
Exit code: 1
Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?at cromwell.engine.workflow.WorkflowDockerLookupActor.cromwell$engine$workflow$WorkflowDockerLookupActor$$handleLookupFailure(WorkflowDockerLookupActor.scala:279) at cromwell.engine.workflow.WorkflowDockerLookupActor$$anonfun$3.applyOrElse(WorkflowDockerLookupActor.scala:93) at cromwell.engine.workflow.WorkflowDockerLookupActor$$anonfun$3.applyOrElse(WorkflowDockerLookupActor.scala:78) at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:35) at akka.actor.FSM.processEvent(FSM.scala:707) at akka.actor.FSM.processEvent$(FSM.scala:704) at cromwell.engine.workflow.WorkflowDockerLookupActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowDockerLookupActor.scala:45) at akka.actor.LoggingFSM.processEvent(FSM.scala:847) at akka.actor.LoggingFSM.processEvent$(FSM.scala:829) at cromwell.engine.workflow.WorkflowDockerLookupActor.processEvent(WorkflowDockerLookupActor.scala:45) at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:701) at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:695) at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:35) at cromwell.docker.DockerClientHelper$$anonfun$dockerResponseReceive$1.applyOrElse(DockerClientHelper.scala:16) at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:269) at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:270) at akka.actor.Actor.aroundReceive(Actor.scala:539) at akka.actor.Actor.aroundReceive$(Actor.scala:537) at cromwell.engine.workflow.WorkflowDockerLookupActor.aroundReceive(WorkflowDockerLookupActor.scala:45) at akka.actor.ActorCell.receiveMessage(ActorCell.scala:614) at akka.actor.ActorCell.invoke(ActorCell.scala:583) at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:268) at akka.dispatch.Mailbox.run(Mailbox.scala:229) at akka.dispatch.Mailbox.exec(Mailbox.scala:241) at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)[INFO] [12/18/2025 07:26:41.631] [cromwell-system-akka.dispatchers.backend-dispatcher-1467] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]:
echo 'DATABASE' > result.txt
[INFO] [12/18/2025 07:26:41.632] [cromwell-system-akka.dispatchers.backend-dispatcher-1467] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: Calculated TES outputs (found 5):
Output(Some(rc),Some(meta_workflow.Identify_analy.rc),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/rc),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/rc,Some(FILE))
Output(Some(stdout),Some(meta_workflow.Identify_analy.stdout),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/stdout),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/stdout,Some(FILE))
Output(Some(stderr),Some(meta_workflow.Identify_analy.stderr),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/stderr),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/stderr,Some(FILE))
Output(Some(commandScript),Some(meta_workflow.Identify_analy.commandScript),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/script),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/script,Some(FILE))
Output(Some(meta_workflow.Identify_analy.output.0),Some(meta_workflow.Identify_analy.output.0),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/result.txt),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/result.txt,Some(FILE))[INFO] [12/18/2025 07:26:41.632] [cromwell-system-akka.dispatchers.backend-dispatcher-1467] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: Calculated TES inputs (found 1):
cromwell.backend.impl.tes.Input(Some(commandScript),Some(meta_workflow.Identify_analy.commandScript),Some(/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/script),/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/script,Some(FILE),None)[INFO] [12/18/2025 07:26:41.632] [cromwell-system-akka.dispatchers.backend-dispatcher-1467] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]:
echo 'DATABASE' > result.txt
[INFO] [12/18/2025 07:26:46.175] [cromwell-system-akka.dispatchers.backend-dispatcher-1467] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: job id: task-710bdfb8
[INFO] [12/18/2025 07:26:47.921] [cromwell-system-akka.dispatchers.backend-dispatcher-1436] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: Status change from - to Running
[INFO] [12/18/2025 07:32:14.919] [cromwell-system-akka.dispatchers.backend-dispatcher-1436] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: Job task-710bdfb8 is complete
[INFO] [12/18/2025 07:32:14.919] [cromwell-system-akka.dispatchers.backend-dispatcher-1436] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-EngineJobExecutionActor-meta_workflow.Identify_analy:NA:1/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b-BackendJobExecutionActor-meta_workflow.Identify_analy:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(b3c8ad44)meta_workflow.Identify_analy:NA:1]: Status change from Running to Complete
[INFO] [12/18/2025 07:32:16.299] [cromwell-system-akka.dispatchers.engine-dispatcher-47] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b] WorkflowExecutionActor-b3c8ad44-dc3b-4e87-9fe9-97c0db47031b [UUID(b3c8ad44)]: Workflow meta_workflow complete. Final Outputs:
{
"meta_workflow.Identify_analy.out": "/cephfs_data/genostack_v3_dev/genostack_cromwell/cromwell-executions/meta_workflow/b3c8ad44-dc3b-4e87-9fe9-97c0db47031b/call-Identify_analy/execution/result.txt"
}
[INFO] [12/18/2025 07:32:21.193] [cromwell-system-akka.dispatchers.engine-dispatcher-82] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor] WorkflowManagerActor: Workflow actor for b3c8ad44-dc3b-4e87-9fe9-97c0db47031b completed with status 'Succeeded'. The workflow will be removed from the workflow store. -
[INFO] [12/18/2025 07:55:14.436] [cromwell-system-akka.dispatchers.backend-dispatcher-1296] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-6de70bcd-083a-4fd7-9198-9cbb2005dbe5/WorkflowExecutionActor-6de70bcd-083a-4fd7-9198-9cbb2005dbe5/6de70bcd-083a-4fd7-9198-9cbb2005dbe5-EngineJobExecutionActor-untarget_workflow.chemrich:NA:1/6de70bcd-083a-4fd7-9198-9cbb2005dbe5-BackendJobExecutionActor-untarget_workflow.chemrich:NA:1/TesAsyncBackendJobExecutionActor] TesAsyncBackendJobExecutionActor [UUID(6de70bcd)untarget_workflow.chemrich:NA:1]: Status change from Running to Complete
-
2025-12-19 14:46:41.752 [container-3592] INFO c.a.c.redis.MessagePubListener - 消费者消费: {"workflowId":"6d8348ea-1893-4b86-b9f7-d2616826f82c[INFO] [12/19/2025 06:45:22.157] [cromwell-system-akka.dispatchers.engine-dispatcher-83] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/b16ea7b9-0d2d-4f29-9ac0-cc8a0a6722bf/WorkflowExecutionActor-b16ea7b9-0d2d-4f29-9ac0-cc8a0a6722bf] WorkflowExecutionActor-b16ea7b9-0d2d-4f29-9ac0-cc8a0a6722bf [UUID(b16ea7b9)]: Starting amplicon_meta.W01_cleandata", "taskName":"", "status":"start", "type":"workflow", "time":"2025-12-19 14:46:36"}
[INFO] [12/19/2025 06:45:25.109] [cromwell-system-akka.dispatchers.engine-dispatcher-97] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor] WorkflowManagerActor: Successfully started WorkflowActor-6d8348ea-1893-4b86-b9f7-d2616826f82c[INFO] [12/19/2025 06:45:22.157] [cromwell-system-akka.dispatchers.engine-dispatcher-83] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b16ea7b9-0d2d-4f29-9ac0-cc8a0a6722bf/WorkflowExecutionActor-b16ea7b9-0d2d-4f29-9ac0-cc8a0a6722bf] WorkflowExecutionActor-b16ea7b9-0d2d-4f29-9ac0-cc8a0a6722bf [UUID(b16ea7b9)]: Starting amplicon_meta.W01_cleandata
-
5-12-23 06:22:21.512 UTC [26] LOG: database system was interrupted; last known up at 2025-12-23 06:21:21 UTC
2025-12-23 06:22:21.950 UTC [26] LOG: database system was not properly shut down; automatic recovery in progress
2025-12-23 06:22:21.954 UTC [26] LOG: redo starts at 18/9B999808
2025-12-23 06:22:21.955 UTC [26] LOG: invalid record length at 18/9BA06F18: wanted 24, got 0
2025-12-23 06:22:21.955 UTC [26] LOG: redo done at 18/9BA06EF0
2025-12-23 06:22:21.955 UTC [26] LOG: last completed transaction was at log time 2025-12-23 06:22:20.084128+00
2025-12-23 06:22:22.075 UTC [1] LOG: database system is ready to accept connections -
cluster:
id: 807d820b-5c5b-451c-9f52-41b93d5d905a
health: HEALTH_ERR
1 MDSs report oversized cache
1 MDSs are read only
2 MDSs behind on trimming
full ratio(s) out of order
Low space hindering backfill (add storage if this doesn't resolve itself): 10 pgs backfill_toofull
94 pgs not deep-scrubbed in time
69 pgs not scrubbed in timeservices:
mon: 3 daemons, quorum bm,bo,bp (age 13d)
mgr: b(active, since 2w), standbys: a
mds: 1/1 daemons up, 1 hot standby
osd: 51 osds: 51 up (since 13d), 51 in (since 2w); 67 remapped pgsdata:
volumes: 1/1 healthy
pools: 4 pools, 2097 pgs
objects: 279.98M objects, 306 TiB
usage: 619 TiB used, 82 TiB / 701 TiB avail
pgs: 3748313/601598194 objects misplaced (0.623%)
2024 active+clean
57 active+remapped+backfilling
10 active+remapped+backfill_toofull
6 active+clean+scrubbing+deepio:
client: 1.2 MiB/s rd, 100 KiB/s wr, 183 op/s rd, 19 op/s wr
recovery: 52 MiB/s, 37 objects/s -
cluster:
id: 807d820b-5c5b-451c-9f52-41b93d5d905a
health: HEALTH_ERR
1 MDSs report oversized cache
1 MDSs are read only
2 MDSs behind on trimming
full ratio(s) out of order
Low space hindering backfill (add storage if this doesn't resolve itself): 10 pgs backfill_toofull
94 pgs not deep-scrubbed in time
69 pgs not scrubbed in timeservices:
mon: 3 daemons, quorum bm,bo,bp (age 13d)
mgr: b(active, since 2w), standbys: a
mds: 1/1 daemons up, 1 hot standby
osd: 51 osds: 51 up (since 13d), 51 in (since 2w); 67 remapped pgsdata:
volumes: 1/1 healthy
pools: 4 pools, 2097 pgs
objects: 279.98M objects, 306 TiB
usage: 619 TiB used, 82 TiB / 701 TiB avail
pgs: 3748313/601598194 objects misplaced (0.623%)
2024 active+clean
57 active+remapped+backfilling
10 active+remapped+backfill_toofull
6 active+clean+scrubbing+deepio:
client: 1.2 MiB/s rd, 100 KiB/s wr, 183 op/s rd, 19 op/s wr
recovery: 52 MiB/s, 37 objects/s -
Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-attacher:v4.0.0 Image: registry.k8s.io/sig-storage/csi-snapshotter:v6.1.0 Image: registry.k8s.io/sig-storage/csi-resizer:v1.6.0 Image: registry.k8s.io/sig-storage/csi-provisioner:v3.3.0 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-attacher:v4.0.0 Image: registry.k8s.io/sig-storage/csi-snapshotter:v6.1.0 Image: registry.k8s.io/sig-storage/csi-resizer:v1.6.0 Image: registry.k8s.io/sig-storage/csi-provisioner:v3.3.0 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-provisioner:v3.3.0 Image: registry.k8s.io/sig-storage/csi-resizer:v1.6.0 Image: registry.k8s.io/sig-storage/csi-attacher:v4.0.0 Image: registry.k8s.io/sig-storage/csi-snapshotter:v6.1.0 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-provisioner:v3.3.0 Image: registry.k8s.io/sig-storage/csi-resizer:v1.6.0 Image: registry.k8s.io/sig-storage/csi-attacher:v4.0.0 Image: registry.k8s.io/sig-storage/csi-snapshotter:v6.1.0 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 Image: quay.io/cephcsi/cephcsi:v3.7.2 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: quay.io/ceph/ceph:v17.2.5 Image: 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Image: quay.io/calico/kube-controllers:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/node:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/node:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/node:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/node:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/node:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/node:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/cni:v3.16.5 Image: quay.io/calico/node:v3.16.5 Image: k8s.gcr.io/coredns:1.7.0 Image: k8s.gcr.io/coredns:1.7.0 Image: k8s.gcr.io/coredns:1.7.0 Image: k8s.gcr.io/coredns:1.7.0 Image: k8s.gcr.io/coredns:1.7.0 Image: k8s.gcr.io/coredns:1.7.0 Image: k8s.gcr.io/cpa/cluster-proportional-autoscaler-amd64:1.8.3 Image: k8s.gcr.io/kube-apiserver:v1.19.7 Image: k8s.gcr.io/kube-apiserver:v1.19.7 Image: k8s.gcr.io/kube-controller-manager:v1.19.7 Image: k8s.gcr.io/kube-controller-manager:v1.19.7 Image: k8s.gcr.io/kube-proxy:v1.19.7 Image: k8s.gcr.io/kube-proxy:v1.19.7 Image: k8s.gcr.io/kube-proxy:v1.19.7 Image: k8s.gcr.io/kube-proxy:v1.19.7 Image: k8s.gcr.io/kube-proxy:v1.19.7 Image: k8s.gcr.io/kube-proxy:v1.19.7 Image: k8s.gcr.io/kube-proxy:v1.19.7 Image: k8s.gcr.io/kube-scheduler:v1.19.7 Image: k8s.gcr.io/kube-scheduler:v1.19.7 Image: docker.io/library/nginx:1.19 Image: docker.io/library/nginx:1.19 Image: docker.io/library/nginx:1.19 Image: docker.io/library/nginx:1.19 Image: docker.io/library/nginx:1.19 Image: k8s.gcr.io/dns/k8s-dns-node-cache:1.16.0 Image: k8s.gcr.io/dns/k8s-dns-node-cache:1.16.0 Image: k8s.gcr.io/dns/k8s-dns-node-cache:1.16.0 Image: k8s.gcr.io/dns/k8s-dns-node-cache:1.16.0 Image: k8s.gcr.io/dns/k8s-dns-node-cache:1.16.0 Image: k8s.gcr.io/dns/k8s-dns-node-cache:1.16.0 Image: k8s.gcr.io/dns/k8s-dns-node-cache:1.16.0 Image: nvcr.io/nvidia/k8s-device-plugin:v0.17.1 Image: nvcr.io/nvidia/k8s-device-plugin:v0.17.1 Image: nvcr.io/nvidia/k8s-device-plugin:v0.17.1 Image: nvcr.io/nvidia/k8s-device-plugin:v0.17.1 Image: nvcr.io/nvidia/k8s-device-plugin:v0.17.1 Image: nvcr.io/nvidia/k8s-device-plugin:v0.17.1 Image: nvcr.io/nvidia/k8s-device-plugin:v0.17.1 Image: csiplugin/snapshot-controller:v4.0.0 -
docker save registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.5.1 -o csi-node-driver-registrar.tar
docker save quay.io/cephcsi/cephcsi:v3.7.2 -o cephcsi.tgar
docker save registry.k8s.io/sig-storage/csi-attacher:v4.0.0 -o csi-attacher.tar
docker save registry.k8s.io/sig-storage/csi-snapshotter:v6.1.0 -o csi-snapshotter.tar
docker save registry.k8s.io/sig-storage/csi-resizer:v1.6.0 -o csi-resizer.tar
docker save registry.k8s.io/sig-storage/csi-provisioner:v3.3.0 -o csi-provisioner.tar
docker save quay.io/ceph/ceph:v17.2.5 -o ceph1.tar
docker save rook/ceph:v1.10.8 -o ceph.tardocker save quay.io/calico/kube-controllers:v3.16.5 -o kube-controllers.tar
docker save quay.io/calico/cni:v3.16.5 -o cni.tar
docker save quay.io/calico/node:v3.16.5 -o node.tar
docker save k8s.gcr.io/coredns:1.7.0 -o coredns.tar
docker save k8s.gcr.io/cpa/cluster-proportional-autoscaler-amd64:1.8.3 -o cluster-proportional-autoscaler-amd64.tar
docker save k8s.gcr.io/kube-apiserver:v1.19.7 -o apiserver.tar
docker save k8s.gcr.io/kube-controller-manager:v1.19.7 -o manager.tar
docker save k8s.gcr.io/kube-proxy:v1.19.7 -o proxy.tar
docker save k8s.gcr.io/kube-scheduler:v1.19.7 -o scheduler.tar
docker save docker.io/library/nginx:1.19 -o ngins.tar
docker save k8s.gcr.io/dns/k8s-dns-node-cache:1.16.0 -o cache.tar
docker save nvcr.io/nvidia/k8s-device-plugin:v0.17.1 -o plugin.tar
docker save csiplugin/snapshot-controller:v4.0.0 -o controller.tar -
docker load < csi-node-driver-registrar.tar
docker load < cephcsi.tgar
docker load <csi-attacher.tar
docker load < csi-snapshotter.tar
docker load < csi-resizer.tar
docker load < csi-provisioner.tar
docker load <-o ceph1.tar
docker load < -o ceph.tardocker load < kube-controllers.tar
docker load < cni.tar
docker load < node.tar
docker load < coredns.tar
docker load < cluster-proportional-autoscaler-amd64.tar
docker load < -o apiserver.tar
docker load < manager.tar
docker load < proxy.tar
docker load < scheduler.tar
docker load < ngins.tar
docker load < cache.tar
docker load < plugin.tar
docker load <controller.tar -
cluster:
id: 807d820b-5c5b-451c-9f52-41b93d5d905a
health: HEALTH_ERR
full ratio(s) out of order
Low space hindering backfill (add storage if this doesn't resolve itself): 5 pgs backfill_toofull
178 pgs not deep-scrubbed in time
117 pgs not scrubbed in timeservices:
mon: 3 daemons, quorum bm,bo,bp (age 39h)
mgr: a(active, since 39h), standbys: b
mds: 1/1 daemons up, 1 hot standby
osd: 51 osds: 51 up (since 109m), 51 in (since 109m); 59 remapped pgsdata:
volumes: 1/1 healthy
pools: 4 pools, 2097 pgs
objects: 279.97M objects, 306 TiB
usage: 617 TiB used, 84 TiB / 701 TiB avail
pgs: 5001255/601565087 objects misplaced (0.831%)
2028 active+clean
54 active+remapped+backfilling
10 active+clean+scrubbing+deep
5 active+remapped+backfill_toofullio:
client: 338 KiB/s rd, 8.8 MiB/s wr, 175 op/s rd, 7 op/s wr
recovery: 65 MiB/s, 49 objects/s -
datasource:
# SQLite 数据库文件：项目根目录自动生成 cromwell_log.db（对应你的数据库名）
url: jdbc:sqlite:/home/genostack/workspace/CromwellStatus/cromwell_log.db
# SQLite 无用户名密码，留空
username:
password:
driver-class-name: org.sqlite.JDBC
initialization-mode: always # 开启自动执行脚本
schema: classpath:schema.sql # 建表脚本路径 -
ID HOST USED AVAIL WR OPS WR DATA RD OPS RD DATA STATE
0 node1 8480G 2468G 0 0 0 0 exists,up
1 node1 9556G 1392G 20 3438k 18 4128k exists,up
2 node1 8933G 2015G 36 1188k 8 1328k exists,up
3 node1 8795G 2153G 0 0 0 0 exists,up
4 node1 9250G 1698G 0 0 0 0 exists,up
5 node1 8957G 1991G 0 0 0 0 exists,up
6 node1 8772G 2176G 0 2563 0 0 exists,up
7 node2 9247G 1701G 1 7584 0 0 exists,up
8 node2 9939G 1009G 0 0 7 20.2k exists,up
9 node2 9352G 1596G 0 0 0 0 exists,up
10 node2 9.87T 838G 0 2563 0 0 exists,up
11 node2 9656G 1292G 0 0 0 0 exists,up
12 node2 9678G 1270G 0 0 0 0 exists,up
13 node2 9558G 1390G 0 2563 0 0 exists,up
14 node3 9945G 1003G 0 0 0 0 exists,up
15 node3 9762G 1186G 0 0 0 0 exists,up
16 node3 9231G 1717G 0 0 0 0 exists,up
17 node3 9239G 1709G 0 2902 0 0 exists,up
18 node3 9668G 1280G 0 2563 0 0 exists,up
19 node3 9551G 1397G 0 721k 0 0 exists,up
20 node3 9859G 1089G 0 0 0 0 exists,up
21 node8 16.1T 2062G 18 1638k 7 831k exists,up
22 node7 13.1T 1450G 2 1638k 9 844k exists,up
23 node7 12.8T 1780G 0 0 0 0 exists,up
24 node7 13.2T 1283G 0 89.7k 0 0 exists,up
25 node7 12.8T 1731G 0 2563 0 0 exists,up
26 node7 13.4T 1119G 0 0 0 0 exists,up
27 node5 12.5T 2039G 0 2563 0 0 exists,up
28 node5 12.4T 2160G 0 0 0 0 exists,up
29 node5 12.9T 1658G 4 27.4k 0 0 exists,up
30 node5 12.7T 1887G 34 6468k 21 6494k exists,up
31 node5 12.8T 1781G 0 0 0 0 exists,up
32 node5 12.2T 2337G 0 0 0 0 exists,up
33 node5 12.5T 2022G 3 819k 9 842k exists,up
34 node6 13.1T 1443G 0 12.1k 0 0 exists,up
35 node6 12.6T 1935G 0 0 0 0 exists,up
36 node6 13.0T 1527G 1 592k 0 0 exists,up
37 node6 12.5T 2095G 0 195 0 0 exists,up
38 node6 12.8T 1731G 0 0 0 0 exists,up
39 node6 13.4T 1174G 0 2563 0 0 exists,up
40 node6 13.0T 1557G 15 2928k 19 3797k exists,up
41 node8 16.4T 1814G 1 2563 7 832k exists,up
42 node8 15.6T 2574G 0 819 0 0 exists,up
43 node8 15.8T 2346G 0 0 0 0 exists,up
44 node8 16.2T 1979G 76 1524k 9 852k exists,up
45 node8 15.8T 2403G 0 0 0 0 exists,up
46 node8 15.8T 2405G 8 2515k 10 2478k exists,up
47 node8 16.1T 2057G 1 8408 0 0 exists,up
48 node8 16.7T 1448G 0 0 0 0 exists,up
49 node8 15.3T 2888G 0 0 0 0 exists,up
50 node8 16.1T 2045G 0 0 0 0 exists,up -
[root@node1 prod]# kubectl get pod -n genostack-base-dev
NAME READY STATUS RESTARTS AGE
postgres-7cffc9f66-6ngfr 0/1 ContainerCreating 0 17m
postgres-7cffc9f66-fqmzm 0/1 Terminating 0 27m
redis-bd7c6cbb4-gtdz9 1/1 Running 0 30d -
Resource Requests Limits
cpu 46867m (41%) 58400m (52%)
memory 242859107584 (28%) 315783595264 (37%)
ephemeral-storage 0 (0%) 0 (0%)
hugepages-1Gi 0 (0%) 0 (0%)
hugepages-2Mi 0 (0%) 0 (0%)
Events:
Type Reason Age From Message
Normal NodeReady 8m (x252 over 16h) kubelet Node node1 status is now: NodeReady
Normal NodeNotReady 59s (x254 over 16h) kubelet Node node1 status is now: NodeNotReady -
ps -eo pid,stat,cmd | grep -E '^.+ D'
-
[root@node1 account]# ps -eo pid,stat,cmd | grep -E '^.+ D'
382513 Ds /opt/gitlab/embedded/bin/postgres -D /var/opt/gitlab/postgresql/data
382518 Ds postgres: autovacuum launcher process
382519 Ds postgres: stats collector process
385554 D svlogd -tt /var/log/gitlab/redis
385557 D svlogd -tt /var/log/gitlab/sidekiq
385704 D svlogd -tt /var/log/gitlab/node-exporter
385705 D svlogd -tt /var/log/gitlab/gitlab-monitor
385707 D svlogd -tt /var/log/gitlab/prometheus
385722 Ds postgres: gitlab-psql postgres [local] SELECT
385926 D tail --follow=name --retry /var/log/gitlab/nginx/error.log /var/log/gitlab/nginx/current /var/log/gitlab/nginx/gitlab_error.log /var/log/gitlab/nginx/access.log /var/log/gitlab/nginx/gitlab_access.log /var/log/gitlab/prometheus/current /var/log/gitlab/prometheus/state /var/log/gitlab/postgresql/current /var/log/gitlab/postgresql/state /var/log/gitlab/redis/current /var/log/gitlab/redis/state /var/log/gitlab/alertmanager/current /var/log/gitlab/alertmanager/state /var/log/gitlab/redis-exporter/current /var/log/gitlab/redis-exporter/state /var/log/gitlab/gitlab-shell/gitlab-shell.log /var/log/gitlab/sidekiq/current /var/log/gitlab/sidekiq/state /var/log/gitlab/gitlab-monitor/current /var/log/gitlab/gitlab-monitor/state /var/log/gitlab/sshd/current /var/log/gitlab/gitlab-workhorse/current /var/log/gitlab/gitlab-workhorse/state /var/log/gitlab/unicorn/unicorn_stderr.log /var/log/gitlab/unicorn/current /var/log/gitlab/unicorn/unicorn_stdout.log /var/log/gitlab/unicorn/state /var/log/gitlab/gitaly/current /var/log/gitlab/gitaly/state /var/log/gitlab/postgres-exporter/current /var/log/gitlab/postgres-exporter/state /var/log/gitlab/node-exporter/current /var/log/gitlab/node-exporter/state /var/log/gitlab/gitlab-rails/production.log /var/log/gitlab/gitlab-rails/gitlab-rails-db-migrate-2023-02-21-09-56-26.log /var/log/gitlab/gitlab-rails/application.log /var/log/gitlab/gitlab-rails/grpc.log /var/log/gitlab/gitlab-rails/production_json.log /var/log/gitlab/gitlab-rails/api_json.log /var/log/gitlab/logrotate/current /var/log/gitlab/logrotate/state -
SELECT count(*) FROM "METADATA_ENTRY";
SELECT * FROM "METADATA_ENTRY" where "WORKFLOW_EXECUTION_UUID" = 'e845ff2e-95ba-4108-bec5-7b8ece2fe76d' ;
SELECT * FROM "METADATA_ENTRY" where "WORKFLOW_EXECUTION_UUID" = 'e1ae68d6-8c6d-4f91-b970-06e65e57c564' ;