creating custom db causes classification issues

[najoshi]

So I have created a custom database by taking the refseq proteins and adding proteins from a database called RUG2. When I run classification with the regular refseq database on one of my samples, I get about 18M classified reads. When I run the same sample with refseq plus RUG2, I only get about 11K reads. I don't understand why adding proteins to an existing database to create a new database results in so much fewer classifications. I'm happy to share any files you need to debug the issue. Any help would be highly appreciated.