[Bioperl-l] Asking for advice on full EMBL extraction

[brian li]

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";
    $index++;
}
# 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.

Brian


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
>
>