Call input and runtime attributes evaluation failed for ...

Edited July 21, 2020 00:26
3 comments

When running a scatter job, I get error "Call input and runtime attributes evaluation failed for idat2gtc"

The more verbose version of the error says:

Failed to evaluate input 'disk_size' (reason 1 of 1): ValueEvaluator[IdentifierLookup]: No suitable input for 'green_idat_size' amongst {...}

The beginning of the task looks like this:

task idat2gtc {
  input {
    File bpm_file
    File egt_file
    Array[File]+ green_idat_files
    Array[File]+ red_idat_files
    ...

I cannot understand what the error message mean. There is no other information about what went wrong. It is my understanding that there was never any attempt by Cromwell to start a task though. Other tasks from the same scatter array started fine.

This is the URL I use to access the workspace and these are the labels for the job:

caas-collection-name "7d031797-0cee-429f-8028-3fc54b388807"

cromwell-workflow-id "cromwell-27dd1b1f-f507-4363-9f73-e429388e12bf"

submission-id "e73464ef-2d0e-417c-b674-b9a41ae3085e"

workspace-id "7d031797-0cee-429f-8028-3fc54b388807"

I am guessing that maybe Cromwell could not localize some files ... but how do I figure out which file are the offending ones?

Comments

3 comments

Giulio Genovese
- Edited July 21, 2020 00:27
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 workspace. So I assume that somehow someone deleted some files in the Google bucket but the sample.tsv did not get updated. Why is it though that Terra cannot provide the name of the file that Cromwell is unable to localize in the error message?

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Jason Cerrato
- July 21, 2020 15:31
Hi Giulio,

Thanks for the follow-up. We still have a ways to go to make the error messaging more helpful—always a WIP for us! I'm happy to creating a request for the team to put time into improving this error messaging if that's helpful for you. Alternatively, if you're inclined and technically capable, you can feel free to submit a PR for improvements here: https://github.com/broadinstitute/cromwell

Let me know what works best for you.

Kind regards,

Jason

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Giulio Genovese
- July 21, 2020 17:43
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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