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

[Theodore H. Smith]

Oh wait, BLASTMAT is a proper environment variable, right?

So I just need to set those lines into my unix thingy that contains  
the environment variables? I'll do that. I can figure it out myself :)

I thought blast itself actually read .ncbirc.

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?
>>
>> --
>> http://elfdata.com/plugin/
>>
>>
>> _______________________________________________
>> Bioinformatics.Org general forum  -   
>> BiO_Bulletin_Board at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>
> _______________________________________________
> Bioinformatics.Org general forum  -   
> BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>
>

--
http://elfdata.com/plugin/