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Hi Ruchi, The only outputs that I recognize to be created are the files in the local cromwell-execitions subfolder "execution". These files are: * docker_cid * script * script.background * script.submit * stderr.background * stdout.backg…
Now again: exit $rc [2018-07-17 20:19:37,84] [info] BackgroundConfigAsyncJobExecutionActor [0b1c68d1CNVSomaticPanelWorkflow.PreprocessIntervals:NA:1]: job id: 24360 [2018-07-17 20:19:37,85] [info] BackgroundConfigAsyncJobExecutionActor [0b1c68d1CNV…
I don’t know if it just needs "a lot of time" to process 11 gene panel seq bam files that are in a mounted local volume.
What I see is that the Status change from - to WaitingForReturnCodeFile is hanging for half a day or longer if I wouldn’t terminate it. Except the first time I ran the workflow, when I got this message about one hour after the Status change from - t…
Please let me know if you need any further information to solve this problem. Thanks, Fred
ls on the execution folder: docker_cid script.kill stderr.kill rc script.submit stdout.background script stderr stdout.kill script.background stderr.background
* Cromwell is running locally * In myWorkflow_inputs I define the docker image for GATK: broadinstitute/gatk:18.104.22.168 including a mounted volume with all data files * There is a cromwell-workflow-log * ls for call-PreprocessIntervals: execution in…