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

[Jason Stajich]

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::StandAloneBlast=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::StandAloneBlast=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
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu