[Bioperl-l] Trouble in executing StandAloneBlast on Win2000

[Takeshi Sasayama]

Hi Brian,

Thank you very much for your suggestion. The Win2000 PC has 1 hard
disk(115GB) and there is 94.5GB free space. I didn't check free disk space
during the search  because there was still 800MB unused physical memory and
I thought this is not virtual memory trouble due to disk space shortage.

Upgrading to 1.2 may be good solution. Actually I once upgraded to Ver.1.2
on Linux machine to test possibility to avoid another bug (which is already
posted bug 1156 and 1240) but failed in running the script (Err like
"WrapperBase was not found" was shown. So I thought there might have been
much change between 1.0.2 and 1.2, and decided to use 1.0.2 and reinstalled.
The multiple database bug 1156 seemed not to be fixed in 1.2 and I don't
know if this trouble is fixed in 1.2, but maybe I should try Ver.1.2 again.

Thanks
Takeshi Sasayama

----- Original Message -----
From: "Brian Osborne" <brian_osborne at cognia.com>
To: "Takeshi Sasayama" <sasayama at lmi.hitachi-sk.co.jp>
Cc: <bioperl-l at bioperl.org>
Sent: Thursday, February 20, 2003 10:28 AM
Subject: Re: [Bioperl-l] Trouble in executing StandAloneBlast on Win2000


> 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 ######
> >
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> >