Thank you both so much for your help @Nicholas_Bokulich and @llenzi (you're welcome to jump in any time!) Sorry for the delay here, I was troubleshooting after I made a couple discoveries
Ok, so I did some digging and I think there is definitely a big mismatch error which is causing my issue where a large portion of the taxonomy labels matching the ids were somehow lost in the creation of the taxonomy file.
@Nicholas_Bokulich, I ran your initial code below and sent it to a file because there was a ton of output. After running a line count, I got the following result: 3196041
This made me do a word count command on my taxonomy file and then the rep_set_99_rdp.fa and the taxonomy file was MUCH smaller (by like 2 million lines haha)
So I think the error was that somehow when I was converting the taxonomy file in python and sending back to my server , a large chunk of the information was truncated.
I went back and did all of the editing in Unix, imported to a qza file without issue and was able to do the vsearch and taxonomy classification! I will have to figure out how to remove the "subclass" "suborder" etc. because this is confusing QIIME2 view and making it seem like theres several "levels".
Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Actinobacteridae;subclass;Actinomycetales;order;Actinomycineae;suborder;Actinomycetaceae;family;Actinomyces
Is there a way to take out the suborder and subclass with the corresponding taxonomic names in unix?
This is a small head of my taxonomy file now (the file is now formatting with tax is then tab and taxonomy)
S000494589 Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Acidimicrobidae;subclass;Acidimicrobiales;order;"Acidimicrobineae";suborder;Acidimicrobiaceae;family;Acidimicrobium;genus
S000632122 Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Acidimicrobidae;subclass;Acidimicrobiales;order;"Acidimicrobineae";suborder;Acidimicrobiaceae;family;Acidimicrobium;genus
S000632121 Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Acidimicrobidae;subclass;Acidimicrobiales;order;"Acidimicrobineae";suborder;Acidimicrobiaceae;family;Acidimicrobium;genus
S000541758 Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Acidimicrobidae;subclass;Acidimicrobiales;order;"Acidimicrobineae";suborder;Acidimicrobiaceae;family;Acidimicrobium;genus
Thank you again, I can't believe this was the issue all along 