[Bioperl-l] Bio::DB::GenBank under mod-perl

[Mark Wilkinson]

Hi all, 

Has anyone else experienced a problem using Bio::DB::GenBank under
mod-perl?  The symptoms are that after a few hours the server is no
longer able to find the Bio::SeqIO::genbank module (in fact, the entire
bioperl-live folder suddenly disappears from @INC as far as I can tell!)

I've tried hammering on the server to see if I can make it fail, but it
works every time... it is only after a certain amount of time that it
stops working.  A server restart solves the problem.  My other scripts
(in the same package) all continue working just fine throughout, it is
only the ones that use Bio::DB::GenBank that start to fail.

Any ideas?  Is there anything that could obviously time-out in the
sequence retrieval mechanism?  I've put some debugging lines into the
script to see if I can watch what happens when it fails, so I might have
more info on the bug(?) later, but perhaps others have noticed this
problem already and have a solution...

Mark

-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae