[Bioperl-l] Zombie processes with GenBank get_Seq_by_acc()

[O'car Johann Campos]

Kevin Brown <Kevin.M.Brown <at> asu.edu> writes:

> 
> Seeing your code might help. They could just be forked children waiting
> for the script to exit before they go away or something else forked them
> and failed to clean up before quitting.
> 
> > -----Original Message-----
> > From: bioperl-l-bounces <at> lists.open-bio.org [mailto:bioperl-l-
> > bounces <at> lists.open-bio.org] On Behalf Of Belaid MOA
> > Sent: Tuesday, May 10, 2011 1:41 PM
> > To: bioperl-l <at> lists.open-bio.org
> > Subject: [Bioperl-l] Zombie processes with GenBank get_Seq_by_acc()
> > 
> > 
> > Dear All,
> >   I installed the latest version of BioPerl and I ran a very simple
> > code: it goes through each line (an ACC) in a file and uses GenBank to
> > get the sequence
> > via get_Seq_by_acc(). A look at ps shows that there were a lot of
> > zombie processes (with <defunct> attribute) created. The list grows
> > with the time.
> > This means that Bio:DB:GenBank is forking and not cleaning the
> > children. Is there any way to overcome the issue? Moreover, is there
> > any way
> > to specify the number of forked processes?
> > 
> > With best regards,
> > -Belaid.
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l <at> lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

Kevin, Belaid, All:

        Recently I've been working with genbank too and ran a code to get
Genbank info from accession numbers, I also noticed the weird behavior and the
zombie processes that are in the background, altough the code works and I get
the info I need there are a lot of zombie processes in the background and for
example running this task with 8000 accession numbers would be a pain where you
all know. I'm not a bioperl expert and I may be missing some piece of code to
quit the forked children as may be happening to belaid, so this is my piece of
code in case any get and idea why is this happening.

http://pastebin.com/Zq88cpwb

Thanks in advance.
Cheers.

O'car.