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

[O'car Campos]

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.
>>
>>
>>
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>
>