Hi @MVEverett, I just wanted to point out that you can pull all of the taxonomy from silva without using "hard mode", as mentioned here. See the qiime rescript get-silva-data --help.
Note: when using the default ranks... the --p-rank-propagation will use all the ranks available prior to subsetting the ranks you want.
The default ranks are mainly set for Bacteria and Archaea, but it is best to use other ranks for various clades of Eukaryotes.
Just modify the --p-ranks flag:
qiime rescript get-silva-data \
--p-ranks domain superkingdom kingdom subkingdom superphylum phylum subphylum infraphylum superclass class subclass infraclass superorder order suborder superfamily family subfamily genus \
--p-rank-propagation \
--p-version 138.2 \
--p-target SSURef_NR99 \
--output-dir silva-138.2-all-ranks.qza \
--verbose
Note: the --p-ranks flag is also available in qiime rescript get-ncbi-data and get-pr2-data.
-Cheers!