I'm wondering if anyone has stumbled upon this issue I'm having with blast. I have a set of contigs I'm blasting against NCBI's NR blast database, and the blast report I get back has a blank field for the subject for the hits I get.
These are the blast commands I am using:
blastx -subject blastdb/nr.pal -query 0.fa -out 0.blast.out blastx -db blastdb/nr.pal -query 0.fa -out 0.blast.out
I have ended up with output like this:
BLASTX 2.2.25+ Query= 5350 787 3793 Length=787 Subject= Length=124 Score = 13.9 bits (24), Expect = 1.9 Identities = 4/6 (67%), Positives = 6/6 (100%), Gaps = 0/6 (0%) Frame = +1 Query 763 IPLQSF 780 +PL+SF Sbjct 85 MPLESF 90 Score = 11.9 bits (19), Expect = 7.3 Identities = 4/9 (45%), Positives = 6/9 (67%), Gaps = 0/9 (0%) Frame = +1 Query 463 PENFV*SSP 489 P++ SSP Sbjct 43 PDBSWISSP 51
As you can see the Subject= is empty in these results.
I have tried changing the output to blastxml, I've tried downloading the fasta file for NR, and formatting that into a blast database, and I still end up with the same situation. My question, is there some option I'm missing from blast that omits the subject, or a different way to specify the blastdb?
I'm running NCBI blast 2.2.25+, and using the NR file and databases from NCBI.
Thanks in advance!