[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:
[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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