Where i can get task logs before task is completed?

Hello. I use cromwell to execute WDL workflows.
There are stderr and stdout files for each task in workflow, but they are empty until task is done. Is there any way to get stdout and stderr earlier?

Answers

  • KateNKateN Cambridge, MAMember, Broadie, Moderator

    Continuously updating views of the stderr and stdout files for tasks in a workflow is a feature handled by the backend you are using to execute your workflow. On the local backend (i.e. running on your own computer), the files do not update until the task finishes.

    On the JES backend, for example, you can access continuously updating views of the stderr file by looking in the metadata,
    image
    then copying the link to the file into your browser. Within the metadata, you should see a line like this:

    "stderr": "gs://url/to/your/stderr/file"
    

    By looking at that link, you will see an updating view of the stderr file, as it is generated.

    For more information on getting started with JES, you can read here.

  • gavvvrgavvvr RussiaMember

    Thank you for the reply, but i am more interested in local backend :)

  • KateNKateN Cambridge, MAMember, Broadie, Moderator

    Then, unfortunately, on the local backend you must wait until your task finishes to view the stderr and stdout files.

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