[Bioperl-l] Asking for advice on full EMBL extraction
Russell.Smithies at agresearch.co.nz
Thu May 7 01:01:13 EDT 2009
Sadly, that's the same code as I ran but I had a Data::Dump in the middle.
Versions of Perl and BioPerl are the same.
We're running RHEL 5 (kernel 2.6.18-92.1.18.el5) with 16GB RAM
If you get a full script running on a smaller dataset, I could probably run it on the bigger stuff and give you back tab-separated (or is that tab\tseparated ?) data for loading into your db.
> -----Original Message-----
> From: brian li [mailto:brianli.cas at gmail.com]
> Sent: Thursday, 7 May 2009 4:50 p.m.
> To: Smithies, Russell
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Asking for advice on full EMBL extraction
> Dear Russell,
> My example code is as following. I omit the parse process and these
> lines give me "Segmentation Fault" too.
> # Start of code
> my $seqio = Bio::SeqIO->new(-file => 'rel_ann_mus_01_r99.dat',
> -format => 'EMBL');
> my $index = 1;
> while (my $seq = $seqio->next_seq)
> print "Dealing with entry: $index\n";
> # End
> The platform I run this code on:
> BioPerl 1.6.0
> Perl 5.8.8
> Ubuntu 8.04 LTS Server 64-bit version (Linux 2.6.24-23-server)
> I have monitored the memory usage when I run the code above. There is
> always around 20GB free memory (buffer size counted in) left. So I
> suppose the segfault can't be explained just by memory shortage.
> On Thu, May 7, 2009 at 11:32 AM, Smithies, Russell
> <Russell.Smithies at agresearch.co.nz> wrote:
> > Hi Brian,
> > I hate to say it but it worked OK for me using rel_ann_mus_01_r99.dat.gz and
> simple example Bio::SeqIO code from bugzilla
> > It's not using more than 1GB memory on our server and doesn't segfault.
> > Send me your example code and I'll give it a go if you like.
> > Russell Smithies
> > Bioinformatics Applications Developer
> > T +64 3 489 9085
> > E russell.smithies at agresearch.co.nz
> > Invermay Research Centre
> > Puddle Alley,
> > Mosgiel,
> > New Zealand
> > T +64 3 489 3809
> > F +64 3 489 9174
> > www.agresearch.co.nz
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