Laura Gauthier
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Recent activity by Laura Gauthier
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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...
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- 3 comments
- 0 votes
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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
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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...
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- 4 comments
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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 ...
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- 2 comments
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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 ...
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- 2 comments
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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
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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...
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- 5 comments
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Terra API workaround?
I have a workflow I'm running on a set of ~1500 samples. The workflow failed, but Job Manager won't give me any information. I get a 500 error. From the Swagger API page, the metadata is too big...
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- 2 comments
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Bug report: sharing new workflow versions
I shared a method config with a collaborator, but continue iterating on the method, creating several more versions. I didn't redact any old versions. My collaborator can't update his existing con...
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- 3 comments
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Can a sample list have an attribute that is a sample list?
I'm trying to set up a gCNV "case" workflow where a set of samples are (effectively) evaluated against a panel of normals. The panel is generated by a workflow on a sample set entity and its outpu...
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