[ensembl-dev] runtime error?

[Nathalie Conte]

Hi, Could I have some help with this please?
Thanks
N
On 21 Oct 2014, at 09:55, Nathalie Conte <nconte at ebi.ac.uk> wrote:

> 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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