Removing features assigned as bacteria (0_Bacteria) but no other taxanomic classifications

Dear QIIME 2 gurus,

Does anyone know how to remove features that are assigned as bacteria but have no other taxanomic classifications? I've used the code below. It successfully removed all non-bacterial sequences from my feature table. However, I'm still seeing some unclassified bacteria (see snapshot). Not sure how I can modify my code to exclude those as well.

qiime taxa filter-table
--i-table table.qza
--i-taxonomy taxonomy_file.qza
--p-exclude mitochondria, chloroplast, 0_Unassigned, 1_Unassigned
--o-filtered-table filtered-table.qza

Any help would be much appreciated! Thanks!

In your case, it looks like the best way to do this would be to add the following line:

--p-include D_1__

So that only features assigned to at least phylum level (or whatever taxonomic level you pass to the include parameter) will be retained.

The other option is to use --p-mode exact to specify that any include/exclude terms must be matched exactly. Then you can use --p-exclude D_0__Bacteria to explicitly drop any features with that exact label. But that requires a second step (since you could, but might not want to use exact terms for the other exclude patterns that you are currently using).

I hope that helps!


Thanks, @Nicholas_Bokulich! I appreciate the help!

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