Output for execution of GATK using the Cromwell engine

Contributors

The execution of GATK using the Cromwell engine produced the following sample output.

[root@genomics1 genomics]# java -jar  cromwell-65.jar run /mnt/genomics/GATK/seq/ghplo.wdl  --inputs /mnt/genomics/GATK/seq/ghplo.json
[2021-08-18 17:10:50,78] [info] Running with database db.url = jdbc:hsqldb:mem:856a1f0d-9a0d-42e5-9199-5e6c1d0f72dd;shutdown=false;hsqldb.tx=mvcc
[2021-08-18 17:10:57,74] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2021-08-18 17:10:57,75] [info] [RenameWorkflowOptionsInMetadata] 100%
[2021-08-18 17:10:57,83] [info] Running with database db.url = jdbc:hsqldb:mem:6afe0252-2dc9-4e57-8674-ce63c67aa142;shutdown=false;hsqldb.tx=mvcc
[2021-08-18 17:10:58,17] [info] Slf4jLogger started
[2021-08-18 17:10:58,33] [info] Workflow heartbeat configuration:
{
  "cromwellId" : "cromid-41b7e30",
  "heartbeatInterval" : "2 minutes",
  "ttl" : "10 minutes",
  "failureShutdownDuration" : "5 minutes",
  "writeBatchSize" : 10000,
  "writeThreshold" : 10000
}
[2021-08-18 17:10:58,38] [info] Metadata summary refreshing every 1 second.
[2021-08-18 17:10:58,38] [info] No metadata archiver defined in config
[2021-08-18 17:10:58,38] [info] No metadata deleter defined in config
[2021-08-18 17:10:58,40] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2021-08-18 17:10:58,40] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2021-08-18 17:10:58,44] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2021-08-18 17:10:58,44] [warn] 'docker.hash-lookup.gcr-api-queries-per-100-seconds' is being deprecated, use 'docker.hash-lookup.gcr.throttle' instead (see reference.conf)
[2021-08-18 17:10:58,54] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2021-08-18 17:10:58,58] [info] SingleWorkflowRunnerActor: Version 65
[2021-08-18 17:10:58,58] [info] SingleWorkflowRunnerActor: Submitting workflow
[2021-08-18 17:10:58,64] [info] Unspecified type (Unspecified version) workflow 3e246147-b1a9-41dc-8679-319f81b7701e submitted
[2021-08-18 17:10:58,66] [info] SingleWorkflowRunnerActor: Workflow submitted 3e246147-b1a9-41dc-8679-319f81b7701e
[2021-08-18 17:10:58,66] [info] 1 new workflows fetched by cromid-41b7e30: 3e246147-b1a9-41dc-8679-319f81b7701e
[2021-08-18 17:10:58,67] [info] WorkflowManagerActor: Starting workflow 3e246147-b1a9-41dc-8679-319f81b7701e
[2021-08-18 17:10:58,68] [info] WorkflowManagerActor: Successfully started WorkflowActor-3e246147-b1a9-41dc-8679-319f81b7701e
[2021-08-18 17:10:58,68] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2021-08-18 17:10:58,70] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2021-08-18 17:10:58,76] [info] MaterializeWorkflowDescriptorActor [3e246147]: Parsing workflow as WDL draft-2
[2021-08-18 17:10:59,34] [info] MaterializeWorkflowDescriptorActor [3e246147]: Call-to-Backend assignments: helloHaplotypeCaller.haplotypeCaller -> Local
[2021-08-18 17:11:00,54] [info] WorkflowExecutionActor-3e246147-b1a9-41dc-8679-319f81b7701e [3e246147]: Starting helloHaplotypeCaller.haplotypeCaller
[2021-08-18 17:11:01,56] [info] Assigned new job execution tokens to the following groups: 3e246147: 1
[2021-08-18 17:11:01,70] [info] BackgroundConfigAsyncJobExecutionActor [3e246147helloHaplotypeCaller.haplotypeCaller:NA:1]: java -jar /mnt/genomics/cromwell-executions/helloHaplotypeCaller/3e246147-b1a9-41dc-8679-319f81b7701e/call-haplotypeCaller/inputs/-179397211/gatk-package-4.2.0.0-local.jar \
     HaplotypeCaller \
    -R /mnt/genomics/cromwell-executions/helloHaplotypeCaller/3e246147-b1a9-41dc-8679-319f81b7701e/call-haplotypeCaller/inputs/604632695/workshop_1906_2-germline_ref_ref.fasta \
    -I /mnt/genomics/cromwell-executions/helloHaplotypeCaller/3e246147-b1a9-41dc-8679-319f81b7701e/call-haplotypeCaller/inputs/604617202/workshop_1906_2-germline_bams_father.bam \
    -O fatherbam.raw.indels.snps.vcf
[2021-08-18 17:11:01,72] [info] BackgroundConfigAsyncJobExecutionActor [3e246147helloHaplotypeCaller.haplotypeCaller:NA:1]: executing: /bin/bash /mnt/genomics/cromwell-executions/helloHaplotypeCaller/3e246147-b1a9-41dc-8679-319f81b7701e/call-haplotypeCaller/execution/script
[2021-08-18 17:11:03,49] [info] BackgroundConfigAsyncJobExecutionActor [3e246147helloHaplotypeCaller.haplotypeCaller:NA:1]: job id: 26867
[2021-08-18 17:11:03,53] [info] BackgroundConfigAsyncJobExecutionActor [3e246147helloHaplotypeCaller.haplotypeCaller:NA:1]: Status change from - to WaitingForReturnCode
[2021-08-18 17:11:03,54] [info] Not triggering log of token queue status. Effective log interval = None
[2021-08-18 17:11:23,65] [info] BackgroundConfigAsyncJobExecutionActor [3e246147helloHaplotypeCaller.haplotypeCaller:NA:1]: Status change from WaitingForReturnCode to Done
[2021-08-18 17:11:25,04] [info] WorkflowExecutionActor-3e246147-b1a9-41dc-8679-319f81b7701e [3e246147]: Workflow helloHaplotypeCaller complete. Final Outputs:
{
  "helloHaplotypeCaller.haplotypeCaller.rawVCF": "/mnt/genomics/cromwell-executions/helloHaplotypeCaller/3e246147-b1a9-41dc-8679-319f81b7701e/call-haplotypeCaller/execution/fatherbam.raw.indels.snps.vcf"
}
[2021-08-18 17:11:28,43] [info] WorkflowManagerActor: Workflow actor for 3e246147-b1a9-41dc-8679-319f81b7701e completed with status 'Succeeded'. The workflow will be removed from the workflow store.
[2021-08-18 17:11:32,24] [info] SingleWorkflowRunnerActor workflow finished with status 'Succeeded'.
{
  "outputs": {
    "helloHaplotypeCaller.haplotypeCaller.rawVCF": "/mnt/genomics/cromwell-executions/helloHaplotypeCaller/3e246147-b1a9-41dc-8679-319f81b7701e/call-haplotypeCaller/execution/fatherbam.raw.indels.snps.vcf"
  },
  "id": "3e246147-b1a9-41dc-8679-319f81b7701e"
}
[2021-08-18 17:11:33,45] [info] Workflow polling stopped
[2021-08-18 17:11:33,46] [info] 0 workflows released by cromid-41b7e30
[2021-08-18 17:11:33,46] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2021-08-18 17:11:33,46] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2021-08-18 17:11:33,46] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2021-08-18 17:11:33,46] [info] Aborting all running workflows.
[2021-08-18 17:11:33,46] [info] JobExecutionTokenDispenser stopped
[2021-08-18 17:11:33,46] [info] WorkflowStoreActor stopped
[2021-08-18 17:11:33,47] [info] WorkflowLogCopyRouter stopped
[2021-08-18 17:11:33,47] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2021-08-18 17:11:33,47] [info] WorkflowManagerActor: All workflows finished
[2021-08-18 17:11:33,47] [info] WorkflowManagerActor stopped
[2021-08-18 17:11:33,64] [info] Connection pools shut down
[2021-08-18 17:11:33,64] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2021-08-18 17:11:33,64] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2021-08-18 17:11:33,64] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2021-08-18 17:11:33,64] [info] SubWorkflowStoreActor stopped
[2021-08-18 17:11:33,64] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2021-08-18 17:11:33,64] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2021-08-18 17:11:33,64] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2021-08-18 17:11:33,64] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2021-08-18 17:11:33,64] [info] JobStoreActor stopped
[2021-08-18 17:11:33,64] [info] CallCacheWriteActor stopped
[2021-08-18 17:11:33,64] [info] KvWriteActor Shutting down: 0 queued messages to process
[2021-08-18 17:11:33,64] [info] IoProxy stopped
[2021-08-18 17:11:33,64] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2021-08-18 17:11:33,65] [info] ServiceRegistryActor stopped
[2021-08-18 17:11:33,65] [info] DockerHashActor stopped
[2021-08-18 17:11:33,67] [info] Database closed
[2021-08-18 17:11:33,67] [info] Stream materializer shut down
[2021-08-18 17:11:33,67] [info] WDL HTTP import resolver closed
[root@genomics1 genomics]#