Ncbi Blast Output Missing Subject Name

Question

[Razzmataz]

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!

[Michael]

type ls in your blastdb directory, what is there?

Answer 1

[Damian Kao]

Is there a reason why you are using "nr.pal" as your database instead of just "nr"? Did you rename your nr database files? Try running:

blastx -db blastdb/nr -query 0.fa -out 0.blast.out

[Razzmataz]

I had been getting some errors when I tried that, something about "no database nr present", so I put in the full path to the database alias file. I'll try this again...

[Michael]

actually you might be missing some files there, this error message is not good.

[Razzmataz]

I've actually been able to get this to run without any problems now, similar to the query you have above. Not sure what I did wrong, but I'll chalk it up to only having used WU-BLAST up until recently... Thanks for the help!