Invalid character in sequence: b'U'

[Nicholas_Bokulich]

Hi @LiyingXie,
This is because your sequences consist of RNA, not DNA sequences. Looks like you are trying to import and use the raw SILVA sequences! So you are importing as the wrong data type.

As you are working with SILVA, I recommend using this tutorial for the RESCRIPt plugin, which will make downloading, formatting, and using SILVA much easier:

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for constru…

The outputs of this tutorial — RESCRIPt-formatted SILVA sequences, taxonomy, and taxonomy classifiers — are also available here, which will save you a lot of time:
https://docs.qiime2.org/2020.11/data-resources/

Good luck!