[Bioclusters] How to specify the Matrix value in blastall

[Bala]

Hi All,
       I solved the error, by specifying the 
matrix path in "BLASTMAT" environment varibale.

  but I want to specify the path in my ".ncbirc"
file, my .ncbirc file content in my root directory
is 

 #cat .ncbirc
[NCBI]
Data="/usr/local/sge/db/data/"


but still blastall is not taking the matrix file
from that location, any suggestion?? help??

-bala-





--- Bala <egrpbala@yahoo.com> wrote:
> Hi All,
>        I can able to run blastall when the BLOSUM62 
> file is in the local directory and I am getting the 
> results, if I try to run from some other location
> and giving the path to the BLOSUM62 file it is
> giving
> the following error!
> 
> Command:
> -------
>       #blastall -p blastp -d /usr/local/db/pataa -i
> /usr/local/sge/QUERY  -M /usr/local/db/BLOSUM62
> 
> Error:
> -----
>     [blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> BlastKarlinBlkGappedCalc: BLOSUM80 is a supported
> matrix
> [blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> BlastKarlinBlkGappedCalc: BLOSUM62 is a supported
> matrix
> [blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> BlastKarlinBlkGappedCalc: BLOSUM50 is a supported
> matrix
> [blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> BlastKarlinBlkGappedCalc: BLOSUM45 is a supported
> matrix
> [blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> BlastKarlinBlkGappedCalc: PAM250 is a supported
> matrix
> [blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> BlastKarlinBlkGappedCalc: BLOSUM62_20 is a supported
> matrix[blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> BlastKarlinBlkGappedCalc: BLOSUM90 is a supported
> matrix
> [blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> BlastKarlinBlkGappedCalc: PAM30 is a supported
> matrix
> [blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> BlastKarlinBlkGappedCalc: PAM70 is a supported
> matrix
> ---------------
> 
>   In that error it is searching BLOSUM62 also, help
> me solve this error.
> 
> Thanks,
> Bala.
> 
> 
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