[Bioperl-l] StandAlone BLAST on Windows???

[Chris Fields]

Do you have the database formatted and are your env variables set correctly
in the ncbi.ini file?  From this output,

[NULL_Caption] WARNING: testquery: Unable to open ecoli.nt.nin

it looks like blastall couldn't find the properly formatted database (env
variable not set correctly) or that the database doesn't exist (need to
format using formatdb).  If I remember correctly, the directory containing
your data in your ncbi.ini file (I placed mine in the C:\Windows dir) should
look something like this:

[NCBI] 
Data=C:\Research\blast\data

You might also want to try leaving out the BLASTDIR if it is already set in
ncbi.ini.  If you can't get it working I'll look into it (unless Torsten has
WinXP????). 

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Bornman, Daniel M
> Sent: Friday, April 21, 2006 11:50 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] StandAlone BLAST on Windows???
> 
> Dear BioPerl Listers,
> 
> Does anyone know if the BioPerl StandAloneBlast module works on Windows?
> 
> I have a very simple script that will not work correctly.
> 
> My PATH is set to 'C:\BLASTDB\bin'
> My database, 'ecoli.nt' is in 'C:\BLASTDB\data' directory
> 
> Here is the script:
> 
> ## START ##
> 
> BEGIN{
> $ENV{BLASTDIR} = 'C:\\BLASTDB\\data';
> }
> use strict;
> use Bio::Seq;
> use Bio::Tools::Run::StandAloneBlast;
> 
> my @params = (program  => 'blastn', database => 'ecoli.nt'); my
> $blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
> my $seq_obj = Bio::Seq->new(-id  =>"testquery", -seq
> =>"TTTAAATATATTTTGAAGTATAGATTATATGTT");
> my $report_obj = $blast_obj->blastall($seq_obj); my $result_obj =
> $report_obj->next_result; print $result_obj->num_hits;
> 
> ## END ##
> 
> 
> Here is the error message I get:
> 
> [NULL_Caption] WARNING: testquery: Unable to open ecoli.nt.nin
> 
> ------------- EXCEPTION  -------------
> MSG: blastall call crashed: 256 C:\BLASTDB\bin\blastall.exe -p  blastn
> -d  "\ecoli.nt"  -i  C:\DOCUME~1\Home\LOCALS~1\Temp\QZwYdo9eKx  -o
> C:\DOCUME~1\Home\LOCALS~1\Temp\ADP2OcZw8z
> 
> STACK Bio::Tools::Run::StandAloneBlast::_runblast
> C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:732
> STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
> C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:680
> STACK Bio::Tools::Run::StandAloneBlast::blastall
> C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:536
> STACK toplevel localblast.pl:12
> 
> --------------------------------------
> 
> 
> Thank You,
> 
> Daniel Bornman
> Researcher
> Battelle Memorial Institute
> 505 King Ave
> Columbus, OH 43201
> 614.424.3229
> 
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