Hi qiime community,
I know this problem was reported before here.
I have the same issu (can not find my taxonomy annotation) I did as explained before the following steps:
qiime tools export: ouptput (table.qza and taxonomy.qza) output (feature-table.biom, taxonomy.tsv)
biom add-metadata -i feature-table.biom -o table_with_taxonomy.biom --observation-metadata-fp taxonomy.tsv --sc-separated taxonomy
when I convert my table_with_taxa.biom to a tsv (just to check) I can not find the taxonomy annotation it keeps the ASVs ID (feature ID) see attached.
This problem was reported several times I don’t know what is really the problem;