[Bioperl-l] questions about run StandAloneBlast?

[Marc Logghe]

Hi,
the call mentioned in the error was
"blastall.exe -p blastp -d "\nr" -i"

The database name does not look healthy to me. Don't know whether this is just the error message displaying it like this, or whether it is actually called. In the latter case it will fail for sure.
Guess it is a bug in case the param database => 'nr' is translated into -d "\nr"
But Brian is right, first check out whether your database is indexed, blastall does not take a plain fastafile (eg your nr.fa is not recognized !!!). Try fastacmd -d <database> -I to find out.
Also take care that in case you don't use the full path for your database, blast will look for it relative to the BLASTDB directory. Adjust the environment $BLASTDB if needed.
HTH,

Marc

> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne at cognia.com]
> Sent: Thursday, October 14, 2004 2:46 PM
> To: Sun, Jian; Jason Stajich
> Cc: bioperl
> Subject: RE: [Bioperl-l] questions about run StandAloneBlast?
> 
> 
> 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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