I'm familiar with the BLAST family of software: I've used both the old interface (blastall, formatdb, et al) and the new interface (blastx, makeblastdb, et al). However, I've always used it with in-house databases. I've never tried downloading and using NCBI's non-redundant database...which is what I'm trying to do now.
Turns out someone in our lab recently downloaded the nr and nt databases using the
update_blastdb.pl script, so that saves me that trouble. However, I am having issues when I try to run BLAST against the database.
I created a Fasta file that has a single query sequence in it...maybe several hundred bp long. When I just do a simple command like one of the two below, it runs without any end in sight (consuming a lot of RAM too).
$ blastall -p blastx -i test.fasta -d /data/blast/db/nr -m 7
^C
$ blastall -p blastn -i test.fasta -d /data/blast/db/nt -m 7
^C
So I though 'ok, maybe I'm supposed to point it at the alias file', so I tried the following commands, ending immediately in an error.
$blastall -p blastx -i test.fasta -d /data/blast/db/nr.pal -m 7
[blastall] FATAL ERROR: AT1G51370.2: Database /data/blast/db/nr.pal was not found or does not exist
$ blastall -p blastn -i test.fasta -d /data/blast/db/nt.pal -m 7
[blastall] FATAL ERROR: AT1G51370.2: Database /data/blast/db/nt.pal was not found or does not exist
I've run fastacmd to make sure the databases are working correctly and I don't see any problems ...