I'm trying to process a large transcriptome fasta file with over 50k sequences (just a bit over 53k). I setup a local blast+ instance and the latest nr database (up to nr.25). I started blastx with the following command:
blastx -query fasta.fa -out blastx.xml -outfmt 5 -eval 1e-3 -num_threads 32
So far it's processed only 3500 sequences over 2 days. It's a fairly decent workstation, 2x Xeon E2560 V2's with 128GB of ram. From our previous experience this shouldn't take over a few days, although at this rate it seems like it's going to take a long time. The output is also quite large for only 3500 sequences, it's already at 1.5GB.
How can I optimize blastx for importing into blast2go? I'm currently reading up on how to parallelize blastx, but I'm not sure if there are better options out there.