User

Laura Gauthier

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Recent activity by Laura Gauthier

  • "Invalid" WDL import fails

    Perfectly good WDLs from 6-12 months ago are failing to load. They may still be on draft-3, but I don't know because I can't actually access them.  I'm willing to update to WDL 1.0, but I need to a...

    • 2 followers
    • 8 comments
    • 0 votes

  • Notebook VM service down?

    I can't create a spark VM (i.e. Hail environment) -- I get this error when I should be on the config page to choose memory I deleted my previous runtime, so I have no clusters right now

    • 3 followers
    • 5 comments
    • 1 vote

  • spark VM autopause issue

    I've been taking advantage of the preconfigured Hail runtime for notebooks, which has been lovely.  And I've noticed the runtime will pause after some amount of time, which is great because those c...

    • 2 followers
    • 1 comment
    • 0 votes

  • can't save update to method config

    I made changes to the method in the Broad methods repo and now that I'm trying to update the config, it times out with the following error:   { "causes": [], "exceptionClass": "com.mysql.jdbc.excep...

    • 2 followers
    • 3 comments
    • 0 votes

  • Bug? Workflow shows as succeeded, but outputs were not delocalized

    In the Job History and in Job Manager, my workflow shows as succeeded, but I had a typo in the task outputs, so my outputs were not localized.  How can this be a success?  

    • 3 followers
    • 7 comments
    • 0 votes

  • How can I get my files into the data model?

    Apparently I have exceeded the maximum number of workflow outputs by 1.8%.  I don't know of another way to get an array into the data model and I suspect if I try to read_lines from a FOFN (file of...

    • 2 followers
    • 4 comments
    • 0 votes

  • CNN configs need outputs

    In the CNN featured workspace that Beri set up, the 1-CNN-Variant-Filter-1D and 1-CNN-Variant-Filter-2D configs don't have outputs specified.  This is particularly insidious because the data model ...

    • 2 followers
    • 2 comments
    • 0 votes

  • ContinueWhilePossible not default?

    What is "Will not start job CollectCoverageGCNV.CollectCounts:1:1 when workflow state is 'WorkflowExecutionFailingState' and when 'restarting'=false" ?  I've never seen this one before.  It sounds ...

    • 2 followers
    • 2 comments
    • 0 votes

  • Workflow aborting for 6 days

    Submission c8c89d05-fc8f-4b49-8abb-cf758e4a4098 in workspace broad-firecloud-dsde-methods/gCNV-CMG-test has been "aborting" for six days.  Will this affect anything else in my workspace, e.g. havin...

    • 2 followers
    • 10 comments
    • 0 votes

  • Workflow hung writing to data model

    I have a workflow that finished a couple days ago based on the existence of outputs in the execution directory, but it still hasn't added those outputs to the data model.  This is submission 419778...

    • 2 followers
    • 5 comments
    • 0 votes