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Salida para la ejecución del GATK utilizando el motor Cromwell
Colaboradores
La ejecución de GATK con el motor Cromwell produjo la siguiente salida de muestra.
[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]#