Anyone know what I did wrong with my archae analysis, using the SILVA database for archaea?

[Nicholas_Bokulich]

Hi @osidito91,
Check out this similar topic from today:

Sklearn-classifier bug for archaea 16s amplicons

Hi every one, I used QIIME 2 (201907) for taxonomic classification. I experienced a problem with classification of my archaea targeted 16s rRNA sequences with the plugin feature-classifier classify-sklearn. All the representative reads generated by Vsearch were classified as bacteria while taxonomic classification of the representative reads generated by Deblur seemed normal. So, I tested Sklearn-classifier with 15 archaea 16s rRNA represent reads from Vsearch representative reads. The result …

@SoilRotifer's advice is probably more relevant to your issue (issues with the database and extracting reads from the database) than the follow-up advice I gave in that topic about mixed-orientation reads (though that could definitely be the issue! check it out).