I downloaded nr locally and am trying to BLAST my fasta files against the nr database. I don't get an error but when I check the out file it looks as though it stops early. It stops at the first run and doesn't do a comparison, only prints the reference names, version, and the 1st query. I'm using...
blastall -p blastn -d nr -i inputfile.fasta -o output.out
Is it not finding nr to make a comparison to?
I downloaded the "per-formatted" databases from NCBI, and after unpacking have .phd .phi .phr .pin .pnd .pni .pog .ppd .ppi .psd .psi and .psq files. Are these per-formatted?