[Bioperl-l] questions about run StandAloneBlast?

[Sun, Jian]

Thanks a lot, Joel. I get it work fine now.
Thanks a lot.
Jian

________________________________

From: Joel Martin [mailto:j_martin at lbl.gov]
Sent: Wed 10/13/2004 12:13 PM
To: Sun, Jian
Subject: Re: [Bioperl-l] questions about run StandAloneBlast?



Hello,
        if your database is called nr.fas then you should call it
"nr.fas" instead of "nr".  Also you should have run formatdb on it so
that you have files named  nr.fas.psq etc...

joel

On Wed, Oct 13, 2004 at 11:48:04AM -0500, Sun, Jian wrote:
> 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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