Hello @Hmickelson,
Would you mind sharing this most recent .qzv file?
table-no-mitochondria-exact.qza.qzv (355.6 KB)
Do you think I should choose a different Unite database? Right now I am using all eukaryotes 216 528 version 9.
Hello @Hmickelson,
It looks like you passed "Unassigned, k__unidentified" to the --p-exclude option. You should copy, paste, and run the command given by @gregcaporaso above without changing anything.
table-no-mitochondria-exact.qza.qzv (355.4 KB)
I took the above command and I am still getting the same results, I have also tried different variations to try and exclude but haven't been successful.
Hello @Hmickelson,
What's going on is that the features classified only to the kingdom level as Viridiplantae have actually been removed. But since you specified the --p-mode exact, only those features are being removed. Change to --p-mode contains (or just don't specify it at all because that is the default) and all features that include this kingdom classification will be removed.
Sorry for the confusion.
@colinvwood by changing to the --p-mode contains this did not work but erasing it completely worked!
Thank you so much! This was a big help!