About OTU clustering of fasta files

[Nicholas_Bokulich]

Hi @sooni ,

The error indicates that the file contains invalid lowercase characters. You could convert these to uppercase to continue, but there could be other issues with the file if you are trying to use data that have already been processed.

I would recommend starting with the raw data. The raw data for this study appear to be deposited on SRA:
https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA683584

so you could download and automatically format the data from there using the QIIME 2 plugin q2-fondue:

q2-fondue: Plugin for (meta)data retrieval from SRA

q2-fondue: (meta)data retrieval from SRA made simple Hello QIIMErs! On behalf of the Bokulich Lab team I would like to present to you our brand new plugin: q2-fondue (Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere)! q2-fondue allows you to grab any sequence data from the Sequence Read Archive (SRA) and corresponding metadata, given a list of SRA run accession IDs or BioProject IDs. Naturally, the resulting artifacts can then be directly plugged into …

This might be an easier approach, as you could then also follow the QIIME 2 tutorials from the start instead of figuring out the entry point for starting with FASTA data.

Good luck!