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broadinstitute / cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
http://cromwell.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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Cromwell stalled at waitingforreturncode #7191

Open dianacornejo opened 11 months ago

dianacornejo commented 11 months ago

Hello, I'm trying to run a workflow locally and it gets stalled on BackgroundConfigAsyncJobExecutionActor [5b4a3086Regenie.RegenieStep1WholeGenomeModel:NA:1]: Status change from - to WaitingForReturnCode

I'm using a local backend

I'm attaching the workflow which is written in WDL language

I'm attaching a screenshot of the configuration file and the input files which I provide to cromwell in json format

Screenshot 2023-08-02 at 3 27 39 PM

Also I'm proving the workflow called regenie.txt regenie.txt

Screenshot 2023-08-02 at 3 29 07 PM

I'm providing the full log file as well. regenie.log If I run the commands locally without using a WDL workflow this runs in under 10 seconds in my local computer.

I appreciate any insight.

I'm using cromwell-85.jar and my java version is openjdk version "17.0.6" 2023-01-17 OpenJDK Runtime Environment Temurin-17.0.6+10 (build 17.0.6+10) OpenJDK 64-Bit Server VM Temurin-17.0.6+10 (build 17.0.6+10, mixed mode, sharing)

I'm running this on a MacOS 13.3.1

Thanks a lot

xujiahao778899 commented 8 months ago

Hi,dianacornejo! Have you solved this problem yet？I also encountered this problem. @dianacornejo