The BLAST jobs traditionally found in the PAP Functional Workflow have been tweaked. The BLASTp jobs were the reason that a functional flow took overnight to complete. As of PAP Functional Workflow v2020.07, BLASTp will no longer be run against Bacterial sequences in the NCBI nonredundant (nr) database. By removing BLASTp against all Bacteria (taxid 2) from the jobs list, run times have been decreased to <1 hour from ~12 hours. In fact, a <100 kb phage genome will usually be completely analyzed in only ~20 minutes.
We consider this a major improvement in the overall standard operating procedure for phage annotation. Fear not, users can still BLAST their genomes against bacterial sequences using a Custom BLASTp to Apollo Evidence Track workflow or other custom methods.
If you want help performing a custom BLAST job for your phage genome in Apollo, please email the support team with your questions! In the meantime, enjoy the drastically reduced processing time for functional workflow processing.