[Bioperl-l] cannot find path to blastall

James Gregory j1gregor at biomail.ucsd.edu
Tue Mar 15 16:30:25 EST 2005

fixed it, i thought you could manually set the path within the perl 
script.  I just added blastall to usr/bin/local (on a unix machine) and it 
works, except now I'm having other troubles.

i ran
formatdb -i SLR16.1_prot.txt -o T -n subtilis

where SLR16.1_prot.txt is a fasta formatted file.  I get these files from 

subtilis.phr  subtilis.pin  subtilis.psd  subtilis.psi  subtilis.psq

from my understanding the .psq file is the one you want so i have

#create seq object for blast
my $blast_seq = Bio::Seq->new( '-id' => "$seq_name",
                                '-seq' => "$prot_seq");

#set BLAST params
my @params = (program => 'blastp',
               database => '/path/to/file/subtilis.psq');
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);

my $blast_report = $factory->blastall($blast_seq);

but i'm getting this error:

Could not find index files for database 

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: blastall call crashed: 256 /usr/local/bin/blastall -p  blastp  -d 
"/home/j1gregor/transposon/subtilis.psq"  -i  /tmp/onOzNhelp8  -o 

STACK: Error::throw
STACK: Bio::Root::Root::throw 
STACK: Bio::Tools::Run::StandAloneBlast::_runblast 
STACK: Bio::Tools::Run::StandAloneBlast::_generic_local_blast 
STACK: Bio::Tools::Run::StandAloneBlast::blastall 
STACK: GFP_find.pl:85

thanks again,

On Tue, 15 Mar 2005, Brian Osborne wrote:

> James,
> On Unix? Windows? Cygwin? Something else? Also is "/path/to/blastall" the
> actual location of blastall? On a Linux machine this might be something like
> "/usr/local/bin/blastall". We need to know a bit more.
> 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 James Gregory
> Sent: Tuesday, March 15, 2005 4:08 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] cannot find path to blastall
> I'm trying to set up a standalone blast and I'm getting an error message
> that says
> MSG: cannot find path to blastall
> code:
> my @params = (program => 'blastp',
>               database => 'db.psq');
> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> my $path = '/path/to/blastall/';
> $path = $factory->program_path($path);
> my $blast_report = $factory->blastall($blast_seq);
> any help would be appreciated.
> James Gregory
> University of California, San Diego
> Department of Biological Sciences
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list