Dear @Nicholas_Bokulich,
unfortunately there are still some issues in the taxonomic classification step.
From what I can see:
- In the rep-seqs.qza, sequences headers all have the 'samplename_counter' suffix
- In the table.qza, sequences header don't have any suffix
- In the taxonomy.qza, sequences are duplicated: for each sequence, there is one entry with the original header (with its own taxonomy assigned) and one entry with the 'samplename_counter' suffix with 'Unassigned' taxonomy.
Here I report the first lines of taxonomy.qzv visualized in qiime view.
Do you think I am doing something wrong?
Thanks