[Bioperl-l] cannot find path to blastall

[James Gregory]

i think that solved the problem.  but more problems.

[blastall] WARNING:  [000.000]  >BA-124-EB41_B01.ab1.Seq: Unable to open 
BLOSUM62
[blastall] WARNING:  [000.000]  >BA-124-EB41_B01.ab1.Seq: 
BlastScoreBlkMatFill returned non-zero status
[blastall] WARNING:  [000.000]  >BA-124-EB41_B01.ab1.Seq: SetUpBlastSearch 
failed.

do i need to put the entre ./ncbi_toolbox/ncbi/bin into my path 
(usr/local/bin)?  although I don't think BLOSUM62 is there.. couldn't find 
it in the ncbi toolbox.

James

On Tue, 15 Mar 2005, Brian Osborne wrote:

> James,
>
> Does:
>
> my @params = (program => 'blastp',
>              database => '"/home/j1gregor/transposon/subtilis');
>
> work?
>
> 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 4:30 PM
> To: Brian Osborne
> Cc: bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] cannot find path to blastall
>
>
> 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
> formatdb.
>
> 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);
>
>
> #BLAST
> my $blast_report = $factory->blastall($blast_seq);
>
>
> but i'm getting this error:
>
> Could not find index files for database
> /home/j1gregor/transposon/subtilis.psq
>
> ------------- 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
> /tmp/HlsmLpIFrT
>
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/site_perl/5.8.3/Bio/Root/Root.pm:328
> STACK: Bio::Tools::Run::StandAloneBlast::_runblast
> /usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/StandAloneBlast.pm:732
> STACK: Bio::Tools::Run::StandAloneBlast::_generic_local_blast
> /usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/StandAloneBlast.pm:680
> STACK: Bio::Tools::Run::StandAloneBlast::blastall
> /usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/StandAloneBlast.pm:536
> STACK: GFP_find.pl:85
>
> thanks again,
> James
>
> 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);
>>
>> #BLAST
>> 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
>>
>>
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>