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

[Pamela Culpepper]

right.


>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 01:41:12 +0000
>
>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/
>>>
>>>
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>
>--
>http://elfdata.com/plugin/
>
>
>
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