BLAST database error - when changing to new BLAST+ local program

biobio · 02-14-2011, 11:19 PM

Hi,
I used local BLAST a while ago and have problem when changing to the new BLAST+.
I put the .../ncbi-blast-2.2.24+/bin and .../ncbi-blast-2.2.24+/db into $PATH

and execute the command
/local/.../blastp -query input -out output.fa -db nr -evalue 0.001

error returned:
BLAST Database error: No alias or index file found for protein database [nr] in search path [/local/.../ncbi-blast-2.2.24+/bin::]

==========================
What does this error mean?
Has the query input query format changes in the new BLAST+?

maubp · 02-15-2011, 02:30 AM

It can't find your blast database (have you shortened the error message? The search path looks funny). There is an environment variable you can set, or just pass the full path rather than just nr.

biobio · 02-15-2011, 09:06 AM

Thanks for your reply! I've tried putting the full path for nr db, but it seems BLAST still search within my current directory.

But, I found a work-around that I put all my query in the folder of nr database, and now it can work fine.

Although I checked the configuration guide again but cannot find ".ncbirc" file they mentioned on http://www.ncbi.nlm.nih.gov/staff/ta...nix_setup.html

Quote:

Originally Posted by maubp

It can't find your blast database (have you shortened the error message? The search path looks funny). There is an environment variable you can set, or just pass the full path rather than just nr.

rglover · 02-16-2011, 09:06 AM

try setting the environment variable BLASTDB to the location of your database, that should do the trick.

ferreirafm · 06-15-2011, 06:20 AM

There is no need of move your blast database. At least for the linux version of the blast+, setting up the appropriate file's owners and permitions will fix the problem.
G'Luck,
ferreirafm

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02-14-2011, 11:19 PM	#1
biobio Junior Member Location: us Join Date: Feb 2011 Posts: 2	BLAST database error - when changing to new BLAST+ local program Hi, I used local BLAST a while ago and have problem when changing to the new BLAST+. I put the .../ncbi-blast-2.2.24+/bin and .../ncbi-blast-2.2.24+/db into $PATH and execute the command /local/.../blastp -query input -out output.fa -db nr -evalue 0.001 error returned: BLAST Database error: No alias or index file found for protein database [nr] in search path [/local/.../ncbi-blast-2.2.24+/bin::] ========================== What does this error mean? Has the query input query format changes in the new BLAST+?

06-15-2011, 06:20 AM	#5
ferreirafm Junior Member Location: Sao Paulo Join Date: Jun 2011 Posts: 1	There is no need of move your blast database. At least for the linux version of the blast+, setting up the appropriate file's owners and permitions will fix the problem. G'Luck, ferreirafm Last edited by ferreirafm; 06-15-2011 at 06:26 AM.

02-15-2011, 02:30 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	It can't find your blast database (have you shortened the error message? The search path looks funny). There is an environment variable you can set, or just pass the full path rather than just nr.

02-16-2011, 09:06 AM	#4
rglover rg Location: uk Join Date: Dec 2008 Posts: 51	try setting the environment variable BLASTDB to the location of your database, that should do the trick.