[ensembl-dev] runtime error?

[Nathalie Conte]

HI
I am using variation API to fetch all SNPs from ensembl with a phenotype associated to them - 
I am writing the info to a file, and each time I run the script, it will stop after a while and trow this error
error file:
DBD::mysql::st execute failed: MySQL server has gone away at /net/isilon5/ma/home/nconte/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 831.
DBD::mysql::st execute failed: MySQL server has gone away at /net/isilon5/ma/home/nconte/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 831.

this is the out file:
Exited with exit code 110.
Resource usage summary:

    CPU time :               9269.09 sec.
    Max Memory :             62 MB
    Average Memory :         59.93 MB
    Total Requested Memory : -
    Delta Memory :           -
    (Delta: the difference between total requested memory and actual max usage.)
    Max Swap :               377 MB

    Max Processes :          3
    Max Threads :            4

The output (if any) is above this job summary.

Any tips welcome
thanks
Nathalie

script:
> #!/usr/local/bin/perl
> use strict;
> use warnings;
> use DBI;
> use Bio::EnsEMBL::Registry;
> 
> 
> Bio::EnsEMBL::Registry->load_registry_from_db(
>     -host=>"ensembldb.ensembl.org", -user=>"anonymous",
>     -port=>'5306', 'db_version' => 75,);
> open (OUTFILE2, ">/outtest6.txt") or die "problem open OUTfile";
> 
> my $vs_adaptor = Bio::EnsEMBL::Registry->get_adaptor('human','variation','variationset');
> my $vs = $vs_adaptor->fetch_by_name('All phenotype-associated variants');
> my $iterator = $vs->get_Variation_Iterator();
> while ($iterator->has_next()) {
> my $var = $iterator->next();
> my $variant=$var->name();
> my @vfs = @{$var->get_all_VariationFeatures()};
> my $cons=$var->display_consequence ();
> my $source=$var->source;
> my $p_value;
> foreach my $vf (@vfs) {
>  my @pfs = @{$var->get_all_PhenotypeFeatures()};
>   foreach my $pf(@pfs) {
>   $p_value=$pf->p_value;
> print OUTFILE2  $variant, "\t",$cons, "\t",$source, "\t", $p_value, "\n";
> }
> }
> }
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