Identifying Viral Sequences In Next Generation Sequencing Data

I am attempting to find viral sequences in the RNA seq data of sequenced tumors. Currently I have changed bam files into fasta files and have used the refseq viral dataset from NCBI, formatted it as a blast database, installed BLAST locally, and used the fastafiles from the bam files as the query against the viral BLAST database. This is painfully, slow and most of the results I'm getting seem to be expression vectors or other garbage. Any ideas on a better way to do this, or perhaps a better way to filter the results from blast ?

Thanks!!