Issue with LEfSe Analysis in QIIME2 – IndexError

It appears that you are trying to run dokdo tools. Assuming you installed like so:

conda activate qiime2-amplicon-2024.10
pip install git+https://github.com/sbslee/dokdo

You can then run dokdo cli tools as outlined here.

Basically, you'd run the following command (while in your qiime 2 environment) to read the help text:

dokdo prepare-lefse -h

-Cheers!

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