error querying custom database using Blast+

[jgeahlen]

So I am trying to query stomach ETS libraries for my gene of interest. I installed blast ncbi-blast-2.2.26+.dmg on mac OSX lion. I downloaded an ETS library as a .seq file which I converted to a .fsa file and made it into a blast database using makeblastdb which gave me the following files;

TSTOM2.fsa.nhr
TSTOM2.fsa.nin
TSTOM2.fsa.nnd
TSTOM2.fsa.nni
TSTOM2.fsa.nog
TSTOM2.fsa.nsd
TSTOM2.fsa.nsi
TSTOM2.fsa.nsq

These files are in /Users/jgeahlen/NCBI_Blast/db, which is a different directory than the blast files since my computer installed it in a directory I don't have permission to modify via command line.

When I try to blast that database using the script below;

Jessicas-MacBook-Air:db jgeahlen$ blastn -db TSTOM2 -query /Users/jgeahlen/NCBI_Blast/input/human3.fsa -out TSTOM2.out

I get the following error; BLAST Database error: No alias or index file found for nucleotide database [TSTOM2] in search path [/Users/jgeahlen/NCBI_Blast/db::/Users/jgeahlen/NCBI_Blast/db:]

but when I look in /Users/jgeahlen/NCBI_Blast/db, there they are

I have created a .ncbirc file and designated BLASTDB=/Users/jgeahlen/NCBI_Blast/db

Both my query and database were made from nucleotide sequences so that cannot be the issue. Please help!

Thanks,
-Jessie

[kmcarr]

You specified a database name TSTOM2 so BLAST is looking for an index file named TSTOM2.nin (or an alias file named TSTOM2.nal). Your BLAST database name is TSTOM2.fsa. Change your command to '-db TSTOM2.fsa'.

[jgeahlen]

That seems to have solved the problem, thanks!!!

[sfyoung]

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