I've been using blast 2.2.15 for a while, and I recently downloaded blast 2.2.25 on my new computer. I wanted to test the new version of blastall with a lamprey genome database and sequence that works on my old computer; however, the new blastall doesn't seem to be doing anything.
For the command,
blastall -p tblastn -d supercontigs.fa.pal -i fgah.fa
The output is:
TBLASTN 2.2.25 [Feb-01-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
Query= FIBRINOGEN GAMMA CHAIN, HUMAN (411 letters)
Since the output stops before mentioning the database, is my old database format incompatible with the new blastall? I attempted to formatdb my database, but blastall still didn't work. Perhaps I'm improperly using formatdb? I haven't been able to find a lamprey database to redownload and formatdb from scratch.