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run wld files in local cluster
I attended the GATK course in Cambridge (UK) and I am now adapting the 1-CNV_Somatic_Panel wdl files that I downloaded from github. I've changed cnv_common_tasks.wdl, cnv_somatic_panel_workflow.b37.inputs.json and cnv_somatic_panel_workflow.wdl to point out the directory to the bam files, reference and local gatk. When I run the following command in the server
java -jar .../cromwell-44.jar run .../cnv_somatic_panel_workflow.wdl --inputs .../gatk4-somatic-cnvs/cnv_somatic_panel_workflow.b37.inputs.json
I get the following error:
[2019-07-17 16:39:30,78] [error] WorkflowManagerActor Workflow bf30e28a-59cc-4f88-b969-02c020101526 failed (during ExecutingWorkflowState): Job CNVSomaticPanelWorkflow.PreprocessIntervals:NA: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: /rds-d3/user/jml96/hpc-work/test/cromwell-executions/CNVSomaticPanelWorkflow/bf30e28a-59cc-4f88-b969-02c020101526/call-PreprocessIntervals/execution/stderr.
Could not retrieve content: Could not read from /rds-d3/user/jml96/hpc-work/test/cromwell-executions/CNVSomaticPanelWorkflow/bf30e28a-59cc-4f88-b969-02c020101526/call-PreprocessIntervals/execution/stderr: /rds-d3/user/jml96/hpc-work/test/cromwell-executions/CNVSomaticPanelWorkflow/bf30e28a-59cc-4f88-b969-02c020101526/call-PreprocessIntervals/execution/stderr
I tried also to run it with singularity and I get exactly the same message.
Is somebody able to help me to solve this issue?