[BiO BB] Testing blast, getting "Unable to open BLOSUM62" error?

[Pamela Culpepper]

If you are using pre-compiled BLAST (downloaded from NCBI),  if may be 
stopping you from reading the .ncbirc file.  They have a define -- 
NCBI_DONT_USE_LOCAL_CONFIG that could be set to TRUE and that's causing the 
problem.

My .ncbirc file is --

[pac at pam-nb ~]$ more .ncbirc
[NCBI]
data=/home/pac/blast/data

[BLAST]
BLASTDB=/home/pac/blast/db
BLASTMAT=/home/pac/blast/data

and it works fine.

Go to -- http://www.lifeformulae.com/local_blast_graphics/index.html
to see how to compile BLAST for a local machine running Linux.

Pam


However, I have compiled blastall (the blast programs wrapper) from scratch.






>From: "Theodore H. Smith" <delete at elfdata.com>
>Reply-To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "The general forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: Re: [BiO BB] Testing blast, getting "Unable to open BLOSUM62" 
>error?
>Date: Fri, 17 Feb 2006 01:34:51 +0000
>
>Hi Pamela,
>
>copying my files in the data/ directory to the directory that my  custom 
>database is in, did work.
>
>However, your suggestion to use the .ncbirc file made no changes, I  was 
>unable to get that working. This is what I put in my file:
>
>[NCBI]
>Data="/usr/blast/data"
>
>[BLAST]
>BLASTDB="/usr/blast/dbs"
>BLASTMAT="/usr/blast/data"
>
>Removing the quotes made no change.
>
>My blast executables and folders, exist in /usr/blast/ so I have /usr/ 
>blast/blastall as an executable, and /usr/blast/data as a folder  
>containing BLOSUM files and the rest of the usual blast data.
>
>What now? I'd rather be able to blast into a DB in any directory, if  
>possible. Especially with custom DB's, because I'm likely to delete  them 
>as they are computer generated experimental DB's.
>
>Or should I always put my custom DBs in my "/usr/blast/dbs" folder  and be 
>done with it?
>
>
>
>On 16 Feb 2006, at 21:53, Pamela Culpepper wrote:
>
>>The is an environment variable -- BLASTMAT  -- that you can set to  the 
>>location of your matrix file.
>>Otherwise, the data/ directory should contain the filters.
>>
>>Pam
>>
>>>From: "Theodore H. Smith" <delete at elfdata.com>
>>>Reply-To: "The general forum at Bioinformatics.Org"  
>>><bio_bulletin_board at bioinformatics.org>
>>>To: "The general forum at Bioinformatics.Org"  
>>><bio_bulletin_board at bioinformatics.org>
>>>Subject: [BiO BB] Testing blast, getting "Unable to open BLOSUM62"  
>>>error?
>>>Date: Thu, 16 Feb 2006 21:43:10 +0000
>>>
>>>Hi people,
>>>
>>>I've installed blast on my computer. I'm getting some errors using  a  
>>>custom DB.
>>>
>>>ShatterProof% cd /Users/theodore/Desktop/customgene.faa/
>>>ShatterProof% blastall -p blastp -d customgene.txt -i query.txt - o  
>>>result.out
>>>
>>>[NULL_Caption] WARNING:  [000.000]  query: Unable to open BLOSUM62
>>>[NULL_Caption] WARNING:  [000.000]  query: BlastScoreBlkMatFill   
>>>returned non-zero status
>>>[NULL_Caption] WARNING:  [000.000]  query: SetUpBlastSearch failed.
>>>
>>>
>>>however, this example copied from ncbi's website, works just fine:
>>>
>>>ShatterProof% cd /usr/blast/dbs/
>>>ShatterProof% blastall -p blastn -d ecoli.nt -i query.txt -o test.out
>>>
>>>I get a text file containing the result.
>>>
>>>Is that because I'm using blastp in the first attempt, and blastn  in  
>>>the second?
>>>
>>>Where does BLAST expect the BLOSUM62 file to be?
>
>
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