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

[Kevin Brown]

Utilizing keywords like "my", "our", etc... is only useful in perl if
you also "use strict;" in your script. This forces perl to deal with
variable scope and should cause those threads to die when the parent
object goes out of scope. Instead they aren't dying because their parent
object never gets destroyed.

In fact, going through your code showed that you had a large number of
errors such as @lines[$i] is NOT how you get something out of an array.
$lines[$i] is.

http://pastebin.com/vx9Y0GW7

Kevin Brown
Center for Innovations in Medicine
Biodesign Institute
Arizona State University 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of O'car Campos
> Sent: Thursday, May 12, 2011 6:57 AM
> To: Dave Messina
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Zombie processes with GenBank
get_Seq_by_acc()
> 
> Dave:
> 
>        Thanks for checking the code, I tried with what you said,
adding
> a
> "my" to line 18 but I still get the zombies. I was exaggerating with
> the
> 8000 genbank codes, also I didn't know about those other tools I will
> check
> them, thanks for the tip. So I'm still in a zombieland.
> 
> Cheers.
> 
> O'car
> 
> 
> On 12 May 2011 03:22, Dave Messina <David.Messina at sbc.su.se> wrote:
> 
> > Thanks for posting the code, O'car.
> >
> > I haven't tried running it, but one thing that occurs to me is that
> on line
> > 18 when you create your Bio::DB::Genbank object, there's no 'my', so
> those
> > objects may be hanging around longer than you expect. The zombies
may
> be
> > those objects' forked processes for connecting to Genbank. Similar
to
> what
> > Kevin said earlier.
> >
> > But that's all speculation.
> >
> > The other thing I'll say as a general comment is that fetching
> thousands of
> > records from Genbank this way (or really fetching any more than 100)
> is
> > inefficient and probably slow also.
> >
> > Instead you might try using Genbank's own fetching tools,
EUtilities,
> > either directly or via the two BioPerl interfaces to them
> > (Bio::DB::EUtilities and Bio::DB::SoapEUtilities).
> >
> >
> > Dave
> >
> >
> >
> >
> > On Thu, May 12, 2011 at 00:16, O'car Johann Campos
> <ocarnorsk138 at gmail.com
> > > wrote:
> >
> >> 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.
> >>
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l