Hey @kspeer,
If you were to run qiime metadata tabulate on taxonomy_unfiltered.qza do you still see the offending entry? I suspect it will look like this instead: k__Bacteria;p__Bacteroidetes
If I’m remembering correctly, taxa barplot pads out the taxonomy strings to make rendering simpler. In other words k__Bacteria;p__Bacteroidetes;__;__;__;__ is just a side-effect of trying to make the depth match everything else, it’s still really k__Bacteria;p__Bacteroidetes.
However if you saw k__Bacteria;p__Bacteroidetes;c__;o__;f__;g__ (with the prefixes) then that would mean there’s a un-named Greengenes OTU with that taxonomic resolution.
Also, unrelated to what I think is happening, there’s another issue with your command.
If we compare your search string to the list we see that they are not exactly the same:
k__Bacteria;p__Bacteroidetes;__;__;__;__ # Your list
k__Bacteria; p__Bacteroidetes; __; __; __; __ # Your --p-exclude
In particular it looks like your query has spaces in it which the computer considers as different.
If I’m remembering correctly about the behavior of taxa barplot your --p-exclude should look more like:
--p-exclude 'k__Bacteria;p__Bacteroidetes'.
Hope that helps!