Failure running my ML workflows about galaxytools HOT 22 OPEN

Sorry, I just say a general debugging process, not specific to any issue mentioned in this thread. From the stderr report @anuprulez provided, I feel the errors could be cleared by re-cleaning the input TSVs.

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I only see "Failed to communicate with remote job server."

That's a job running error, you'll want to check this with Nate, that is not a tool error.

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@anuprulez I just ran my third workflow (CNN workflow) on galaxy.eu and it failed. Could you please check the log to see what error message we get? Thanks.

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I only see "Failed to communicate with remote job server."

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@kxk302 in the first and third histories, I don't have permission to see those datasets. Can you unlock those?

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Update: I re-ran the third history after the initial failure and it completed successfully.

@anuprulez how do I unlock the datasets? I don't see an option when trying to share history. If you want we can use Gitter to resolve this. Thx

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I see some changes have been made to: https://github.com/goeckslab/Galaxy-ML/tree/master/galaxy_ml very recently

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https://github.com/goeckslab/Galaxy-ML/tree/master/galaxy_ml

Yes, there was a bug fix in Galaxy-ML that was pushed recently.

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Here are the links to all workflows and datasets for histories:

First history:

https://training.galaxyproject.org/training-material/topics/statistics/tutorials/FNN/workflows/
https://zenodo.org/record/4660497/files/X_test.tsv
https://zenodo.org/record/4660497/files/X_train.tsv
https://zenodo.org/record/4660497/files/y_test.tsv
https://zenodo.org/record/4660497/files/y_train.tsv

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Second history:

https://training.galaxyproject.org/training-material/topics/statistics/tutorials/RNN/workflows/
https://zenodo.org/record/4477881/files/X_test.tsv
https://zenodo.org/record/4477881/files/X_train.tsv
https://zenodo.org/record/4477881/files/y_test.tsv
https://zenodo.org/record/4477881/files/y_train.tsv

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Third history:

https://training.galaxyproject.org/training-material/topics/statistics/tutorials/CNN/workflows/
https://zenodo.org/record/4697906/files/X_train.tsv
https://zenodo.org/record/4697906/files/y_train.tsv
https://zenodo.org/record/4697906/files/X_test.tsv
https://zenodo.org/record/4697906/files/y_test.tsv

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You need to re-name the uploaded files and change their type to tabular, before running the workflows. Thx.

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Second history:

https://training.galaxyproject.org/training-material/topics/statistics/tutorials/RNN/workflows/
https://zenodo.org/record/4477881/files/X_test.tsv
https://zenodo.org/record/4477881/files/X_train.tsv
https://zenodo.org/record/4477881/files/y_test.tsv
https://zenodo.org/record/4477881/files/y_train.tsv

I get these errors while running this workflow

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@anuprulez did you downgrade the tool versions in the RNN workflow?

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If you downgrade the tool versions as I documented, it will work.

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I guess the questions is why it stopped working with the new versions of those tools.

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Try to check various package versions in the conda environment, python version as well (make sure python 3.6). The conda includes a lot of members, prone to make errors when a newer package joins the team.

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Thanks @qiagu,

Could you please provide more info on how to do that?

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Try to ensure the classification targets are integers, not float.

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I do not see the errors that Anup sees. I guess the first step would be to get these workflows working with older versions of the tools. Then we can use the new version to re-produce the problem. @anuprulez not sure what your internet connectivity is like, but we could possibly have a Zoom meeting to discuss tomorrow (Friday). I'm free from 8:00 am to 10:100 am EST time.

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I only see "Failed to communicate with remote job server."

That's a job running error, you'll want to check this with Nate, that is not a tool error.

This is run on EU. I remember vaguely Bjorn saying that some jobs are configured to run on GPU and this error would show up then, and the error would go away when job was run on CPU. Am I right @bgruening?

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