The Silva classifier I trained was used for fungal, but the species classification results were all bacteria

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Hi @LiyingXie, sorry about that. I forgot to mention we've recently updated RESCRIPt to work with QIIME 2 version 2021.4 and later. You can pick from one of several prior release versions of RESCRIPt, which often match the associated QIIME 2 version.

Since you are running QIIME 2 2021.2 you can install the appropriate version of RESCRIPT via the following command:

pip install git+https://github.com/bokulich-lab/RESCRIPt.git@2021.2.0

Let us know if this works for you.

-Cheers!
-Mike

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