Yes @arwqiime, we are aware of this and made note of it here.
The --p-level is not meant to be tied to a specific rank. The level is expected to change depending on what collection of ranks you pull from a given database. In fact, you can use all ~19 ranks of SILVA (see qiime rescript get-silva-data --help), and here. We've just been defaulting to the "standard" :
- domain phylum class order family genus
SILVA 144 now defaults to the following (at least for Bacteria and Archaea):
- domain kingdom phylum class order family genus
For SILVA 144, if you install the current PR version I linked previously, you can modify --p-ranks to pull the new default ranks (which I think is what the SILVA folks built their classifiers on):
qiime rescript get-silva-data \
--p-version 144 \
--p-ranks domain kingdom phylum class order family genus \
--output-dir silva-ref-144 \
--verbose
You can also simply use the default, or explicitly modify the above by removing kingdom:
--p-ranks domain phylum class order family genus
^^ this is the current default for RESCRIPt's get-silva-data.
-Mike