[Bioperl-l] blastall and blosum62 problem

[Mariano Latorre A]

I have a standalone blastall and a html version of blast on my server 
and i am having problems with my results:

When I try the HTML version, I submit this pair of sequences 
("sequences.in"):

 >Test1
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
 >Test2
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT

I try a TBLASTX with BLOSUM62 and I get good results.

But I need to use blastall with the script version...so I try with this 
command:

cat sequences.in | blastall  -p tblastx -d /usr/local/blast/data/db1 -M 
BLOSUM62 | more

and I get this errors and warnings:

[blastall] WARNING:  [000.000]  Test1: Unable to open BLOSUM62
[blastall] WARNING:  [000.000]  Test1: BlastScoreBlkMatFill returned 
non-zero status
[blastall] WARNING:  [000.000]  Test1: SetUpBlastSearch failed.
[blastall] WARNING:  [000.000]  Test2: Unable to open BLOSUM62
[blastall] WARNING:  [000.000]  Test2: BlastScoreBlkMatFill returned 
non-zero status
[blastall] WARNING:  [000.000]  Test2: SetUpBlastSearch failed.

But remember this: when I try blastn I get good results again:

cat sequences.in | blastall  -p blastn -d /usr/local/blast/data/db1 -M 
BLOSUM62 | more

I need this working first, then I need to code some perl scripts.

thanks,
Mariano