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Somatic mutation pipeline error at"WorkflowManagerActor Workflow 709e5b32-05c0-4e49-96b7-bc5c4ab56"

suimyesuimye TokyoMember
edited February 12 in Ask the GATK team

Dear GATK team,

I am trying to call somatic mutation by using best practice pipeline for somatic mutation calling. Almost all data was successfully called somatic mutation in VCF files. However, several files were failed to run on the way of pipeline. Here, I picked up to the error strings from logs. Do you have any suggestions why this problem was occurred?

1. gatk docker: broadinstitute/gatk, 123712a62f94
2. GATK: v4.0.8.1
3. openjdk version "1.8.0_191"
4. OpenJDK Runtime Environment (build 1.8.0_191-8u191-b12-2ubuntu0.16.04.1-b12)
5. OpenJDK 64-Bit Server VM (build 25.191-b12, mixed mode

in output log
[2019-02-08 00:55:32,66] [error] WorkflowManagerActor Workflow 709e5b32-05c0-4e49-96b7-bc5c4ab56256 failed (during ExecutingWorkflowState): Job Mutect2.M2:4:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details. Check the content of stderr for potential additional information: /transient/suimye/181016LUAD/180207_singlerun/cromwell-executions/Mutect2/709e5b32-05c0-4e49-96b7-bc5c4ab56256/call-M2/shard-4/execution/stderr. Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2/709e5b32-05c0-4e49-96b7-bc5c4ab56256/call-M2/shard-4/tmp.5a9c12c6

(There is no error information in /call-M2/shared-4/execution/stderr. The pipeline was stopped in the step "shard-4". I copied the last strings in the stderr file.)

Post edited by suimye on


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