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ENH: Mention `--skip-validation` flag when augur export fails validation as workaround for users

Open corneliusroemer opened this issue 1 year ago • 1 comments

Context

Related to #1044, sometimes it seems that export validation can fail despite there not being any obvious problem.

Insiders know that --skip-validation exists in such situations. But we can't expect average users to know all export options.

So it would be nice if we mentioned the existence of --skip-validation at the end of a validation error - as a way to appease if users want to try out whether their tree works in fact.

Possible solution

Validation of 'results/nebraska_hmpxv1/raw_tree.json' failed.

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Validation of results/nebraska_hmpxv1/raw_tree.json failed. 

The tree was still produced, so you can inspect it by dropping into `https://auspice.us`.

But it is not expected to display correctly.

If you find that the tree is still correct, you can prevent validation from throwing an error by adding the `--skip-validation` flag to export.

If you don't understand the reason why validation failed, we encourage you to post on discussion.nextstrain.org with the logs, so we can have a look.

corneliusroemer avatar Sep 16 '22 19:09 corneliusroemer

This would be a great improvement to the error message.

tsibley avatar Sep 19 '22 17:09 tsibley