[Bioperl-l] questions about run StandAloneBlast?

[Brian Osborne]

Jian,

Did you create the index files for nr using formatdb?

Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Sun, Jian
Sent: Wednesday, October 13, 2004 12:48 PM
To: Jason Stajich
Cc: bioperl
Subject: [Bioperl-l] questions about run StandAloneBlast?

Dear Jason;
   I noticed that you replyed many questions related to StandAloneBlast
before, here I have get a problem too when I tried to run blast locally,
hope you can help me.
Below is the code I am testing:
.........
use Bio::Tools::Run::StandAloneBlast;
use strict;
use warnings;

my $filename = 'seqin.fasta';
my @params = ('database' => 'nr',
              'outfile' => 'myblast.txt',
              'program'  => 'blastp',
              '_READMETHOD' => 'Blast');
   my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
   my $seqio = Bio::SeqIO->new(-file   => $filename,
          -format => 'Fasta' );
          my $seqobj = $seqio->next_seq();
   my $report = $factory->blastall($seqobj);
.........

And I get the error message as:
[NULL_Caption] WARING: >tr|Q6QDR2: Could not find index files for database
\nr
------------EXCEPTION------------------------
MSG: blastall call crashed: 256 blastall.exe -p blastp -d "\nr" -i
C:\DOCUME~1\...\.. -o myblast.txt

STACK Bio::Tools::Run::StandAloneBlast::_runblast
c:/perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:751
STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
c:/perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:698
STACK Bio::Tools::Run::StandAloneBlast::blastall
c:/perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:553
STACK toplevel test91304.pl:29
-------------------------------------------------------------------------

The DIR I am working on is C:/program Files/Apache Group/Apache2/cgi-bin, so
all my *.pl files, the download blastall.exe etc and database nr.fas are
under this directory.

Thanks for any help
Jian


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