[Bioperl-l] Newbie StandAloneBlast - too many files?

[Keith Boroevich]

i am using the latest version of biperl (i have the administator upgrade it
less than a week ago)... and i did notice that StandAloneBlast does have
it's own destroy function but I never tried calling the cleanup function
manually.  The files are deleted from the /tmp/ dirctory after each round of
blasts (2 per loop).  I'll try the _io_cleanup.  currently i just reduced
the number of sequences in each run to 20 and call the script multiple
times...

thanks

----- Original Message -----
From: "Jason Stajich" <jason at cgt.mc.duke.edu>
To: "Keith Anthony Boroevich" <kaboroev at sfu.ca>
Cc: <bioperl-l at bioperl.org>
Sent: Wednesday, February 12, 2003 5:14 AM
Subject: Re: [Bioperl-l] Newbie StandAloneBlast - too many files?


> This is a bug in old releases that should be fixed in bioperl-1.2.
>
> You can alternatively call (where $blastfactory is your StandAloneBlast
> object):
>
> $blastfactory->io->_io_cleanup();
>
> before each blastall run to insure files are cleaned up on each round.
>
> -jason
>
> On Wed, 12 Feb 2003, Keith Anthony Boroevich wrote:
>
> > hi,
> > i am running looped stand alone blast of 88 100pb sequences and around
> > the 80th or so sequence i recieve the error...
> >
> >  >Uncaught exception from user code:
> >  >Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp file
> > /tmp/K6eorI51Yw: Too many open files at
> > /usr/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm line 614
> >  >Carp::croak('Error in tempfile() using /tmp/XXXXXXXXXX: Could not
> > create temp...') called at /usr/lib/perl5/5.6.1/File/Temp.pm line 1052
> >  >File::Temp::tempfile('UNLINK', 1, 'DIR', '/tmp') called at
> > /usr/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm line 614
> >  >Bio::Root::IO::tempfile('Bio::Root::IO=HASH(0x8c5989c)') called at
> > /usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm line 706
> >  >
> >
>Bio::Tools::Run::StandAloneBlast::_setinput('Bio::Tools::Run::StandAloneBla
st=HASH(0x8c47024)', 'blastall', 'Bio::Seq=HASH(0x8f91528)') called at
/usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm line 483
> >  >
> >
>Bio::Tools::Run::StandAloneBlast::blastall('Bio::Tools::Run::StandAloneBlas
t=HASH(0x8c47024)', 'Bio::Seq=HASH(0x8f91528)') called at ../bce.pl line 115
> >  >
> >  >[2]+  Exit 24                 ../bce.pl orangutan.fas
> >  >orangutan.blast  (wd: ~/mager/primate)
> >
> > this however is only my testing set and i will "hopefully" be running
> > hundreds to thousands of 100bp sequences through this.  Any suggestions
> > would be gratly appriciated
> >
> > Keith
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
>