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pathway_annotation() long runtime, connecting to KEGG database

Open erikpark opened this issue 1 year ago • 6 comments

Question: Is there a, general, expected runtime for the KEGG database connection step of the pathway_annotation() command?

This is my first time using the package, and I am passing (what I think is) a relatively small number of features, 228, to the annotation step - yet it's been running at the "We are connecting to the KEGG database to get the latest results, please wait patiently." step for ~6 hours.

If this runtime is expected, would it be possible to download the annotations ourselves and pass them to the annotation() command locally?

Thanks for any help you can provide!

erikpark avatar Apr 25 '23 21:04 erikpark