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Old 02-14-2011, 10:19 PM   #1
biobio
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Default 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+?
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Old 02-15-2011, 01:30 AM   #2
maubp
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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.
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Old 02-15-2011, 08:06 AM   #3
biobio
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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 View Post
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.
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Old 02-16-2011, 08:06 AM   #4
rglover
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try setting the environment variable BLASTDB to the location of your database, that should do the trick.
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Old 06-15-2011, 05:20 AM   #5
ferreirafm
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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 05:26 AM.
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