I'm struggling to assign taxonomy to ITS amplicons. I downloaded the UNITE v8 database and imported the reference sequences and taxonomy using the following:
Plugin error from feature-classifier: 'Identifier 227 was reported in taxonomic search results, but was not present in the reference taxonomy.'
I compared the original FASTA and taxonomy files, but didn't find any discrepancy between the 227th sequence and taxonomic ID. Is this an error in the original database, or something with the way I imported these files as q2 artifacts? I also attempted this with the dynamic clustered database and received the same error.
Thanks for the link, Colin! I reformatted the fasta headers, but unfortunately I am getting the same error as before. I also used the developer files as the tutorial pointed out.
I am using the latest Qiime 2 v. 2021.11. Yes, I did try using the 99% and dynamic identity set and got the same error.
Strangely enough, I was able to train a classifier with reference sequences and taxonomy, and then used that to assign taxonomy. I cannot fathom why VSEARCH won't work when training a classifier will.
Luckily this reference dataset is somewhat small compared to Silva, so I can easily use classify-sklearn where normally I would opt to use VSEARCH due to my hardware limitations.