Hi @jrdupuis, welcome to :qiime2:!
Have you tried this approach to make your database? I explicitly use the trnL marker gene as an example (though slightly different primer pair). Some general thoughts and other highlights from the tutorial:
- You'll notice the
--p-queryis far more explicit. This is to make sure I am including the groups I would like to keep, and excluding spurious reference data. - Also, relying solely on PCR / Sequencing primer searches can be problematic.
- Taxonomic miss-annotation is a common problem in reference databases and can affect the resulting consensus taxonomy, and may need to be corrected. For this reason we provide the edit-taxonomy command within RESCRIPt, to help mitigate these issues.
Perhaps run through the tutorial and let us know if this helps?
-Cheers!
-Mike