Giulio Genovese

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3. PreparingJob state consumes most of a task running time, how to avoid?

I am happy to say that the PreparingJob wait time is completely gone from my pipeline(!). I do have a lingering question though. Does it take longer to estimate the size of a file if it is in a mul...

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• July 23, 2020 14:02
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3. PreparingJob state consumes most of a task running time, how to avoid?

If that's the case, there is an easy solution. Those files are all the same size anyway, so I can just change that code to: Float gtc_size = length(gtc_files) * size(gtc_files[0], "GiB") If this ...

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• July 21, 2020 17:48
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3. Call input and runtime attributes evaluation failed for ...

I see, so this is a Cromwell issue rather than a Terra issue. I think I am too swamped right now to take on me another task. Thank you for the explanation though.

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• July 21, 2020 17:43
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3. unable to view status of running job

Can I have some more information about what job metadata I should try to minimize? Is it the metadata passed between workflow and tasks that is overwhelming the job manager? I can take some steps t...

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• July 21, 2020 16:50
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3. unable to view status of running job

I don't understand. I went to this page: http://portal.firecloud.org/#workspaces/mccarroll-mocha-terra/mocha Then had to switch to the legacy interface (which is so much better than Terra interface...

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• July 21, 2020 15:01
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3. unable to view status of running job

I am having the same issue: Submission ID: 84b157be-a26e-40e6-9f6e-5af12b39976f Workflow ID: 5029f6c6-2069-449d-9a70-38afd5450366 I was able to monitor the job until it failed. I know it failed be...

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• July 21, 2020 01:43
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3. Call input and runtime attributes evaluation failed for ...

It turns out that what is happening is simply that one of the files in the Array[File]+ green_idat_files array is missing. These were files provided to me in the sample.tsv table from another works...

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• Edited July 21, 2020 00:27
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3. PreparingJob state consumes most of a task running time, how to avoid?

This is the URL I use to access the workspace.

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• July 16, 2020 16:51
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3. write_lines()/write_map()/write_tsv()/write_json() fail when run in a workflow rather than in a task

Hi Jason, So Chris Whelan has explained to me that this is the result of a deliberate configuration of Cromwell on Terra that does not allow to serialize tables on the machine that runs the Cromwel...

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• July 14, 2020 21:38
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3. Terra fails to delocalize files listed through read_lines()

Hi Jason, Thank you for your prompt reply. I have found a workaround that effectively is a solution for me, but I would say that this is still an issue for the community. It turns out this is a kno...

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• Edited July 14, 2020 21:46
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