Why does most my sample has uncategorized bacteria?

Hi @amm59063,

Can you please provide the exact commands you ran up until this point? Even better can you provide the QZV file from this barplot image? Looking at the provenance information will help us help you. Finally what amplicon region are you using?

Otherwise, these issues often occur because, the incorrect classifier is being used, sequencing reads are not in the same orientation as the reference database, etc.. There are many threads on the forum related to this topic. Here are links to a couple to help get you started:

-Mike