[Bioperl-l] Primer 3: MSG: Can't open RESULTS

[Gregory Drake Wilson]

I am resurrecting a question posted last June (archived here
http://bioperl.org/pipermail/bioperl-l/2004-June/016255.html) regarding
bioperl's usage of Primer3 because the issue continues to plague me. All
of my implementations die reliably after a fixed number of attempts at
generating primers with this error:

------------- EXCEPTION  -------------
MSG: Can't open RESULTS
STACK Bio::Tools::Run::Primer3::run
/usr/lib/perl5/vendor_perl/5.8.2/Bio/Tools/Run/Primer3.pm:360
STACK toplevel ./primer_maker.pl:128

--------------------------------------

The offending line (360) is:
  open (RESULTS, "$executable < $tempfile|") || $self->throw("Can't open
RESULTS");

As the old thread suggests it is probably a numer of open files issue.

> lsof -c pri +Lr
returns an ever increasing amount of entries like:
 primer_ma 28830 gdw1  425u   REG    3,6     1140     0  807353
/tmp/twdZa7turz (deleted)
primer_ba 28830 drakos7  426u   REG    3,6     1170     0  807354
/tmp/QDJv6Mb8iV (deleted)

Does anyone know a way to make sure those file descriptors are cleaned up
after each primer generation?

Greg