[Bioperl-l] Trouble in executing StandAloneBlast on Win2000

[Brian Osborne]

Takeshi,

What is happening to your free disk space as the search progresses? The 
standard answer is upgrade to version 1.2 but in this case the answer 
is a good one, there is a known StandAloneBlast bug in older Bioperl's 
that sounds a lot like your's.

Brian O.


On Thursday, February 20, 2003, at 08:44 AM, Takeshi Sasayama wrote:

> Hi, all
>
>
> I'm a newbie in Bioperl and I have a problem in executing Blast search 
> on
> Windows 2000 using StandAloneBlast. During about 30,000 Blast search, 
> the
> search had slowed down gradually as the search went on.
>
> What I am doing is to execute blastn search for about 30,000 times in a
> loop. The query file is one file of FASTA format (including about 
> 30,000
> sequences of all 50mer length) and the database contains 27,000 
> entries.
> Each search result is saved in a directory as a file named with its 
> sequence
> name.
>
> At first I ran the program on Linux machine (Red Hat Linux 7.2, PenIII
> 500MHz, 128MB RAM, perl v5.6.0, Bioperl-1.0.2, NCBI-Blast2.2.5(linux
> binary)) and finished successfully in 6 hours. After that I modified 
> the
> same program (only PATH handling) and ran on Windows machine (Windows 
> 2000
> professional(SP3), Pentium4 2.53GHz, 1024MB RAM, ActivePerl 
> v5.6.1(build
> 628), Bioperl-1.0.2, NCBI-Blast2.2.5(windows binary)). This was 
> reproducible
> on the same PC and on another Win 2000 PC. I thought that some kind of
> resource was exhausted but the memory was left free enough(800MB). I 
> don't
> know what causes this trouble .
>
> Does anyone have similar experience?
> Any comments, suggestions, ideas are very much welcome. The script 
> that I
> wrote is essentially below.
>
> Thanks in advance!
> Takeshi Sasayama
>
> ###### Code starts here ######
> BEGIN {
> $ENV{BLASTDIR} = 'C:\\blast';
> $ENV{BLASTDATADIR} = 'C:\\db\\Ensembl\\10.30';
> }
>
> use Bio::Tools::Run::StandAloneBlast;
> use Bio::Seq;
> use Bio::SeqIO;
> use strict;
>
> my $database_file = 'Homo_sapiens.cdna.fa';
> my $queryfile = queryfile.fa';
>
> # parameters
> my $expect_value = 1;
> my $filter_query_sequence = 'F';
> my $one_line_description = 100;
> my $alignments = 100;
> my $strands = 1;
> my @params = ('program' => 'blastn', 'database' => $database_file);
> my $progress_interval = 100;
>
> # create factory object and set parameters
> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> $factory->e($expect_value);
> $factory->F($filter_query_sequence);
> $factory->v($one_line_description);
> $factory->b($alignments);
> $factory->S($strands);
>
> # get query
> my ($in, $queryseq, $blast_report, $outfile);
> $in = Bio::SeqIO->new( -file => $queryfile, -format => 'Fasta');
> while ($queryseq = $in->next_seq()) {
>  $outfile = 'outfiledir'."\\".$queryseq->id;
>  $factory->outfile($outfile);
>  $blast_report = $factory->blastall($queryseq);
> }
> ###### Code ends here ######
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>