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

Theodore H. Smith delete at elfdata.com
Thu Feb 16 20:34:51 EST 2006

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:



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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