[ensembl-dev] runtime error?

Andy Yates ayates at ebi.ac.uk
Fri Oct 31 10:08:13 GMT 2014


Hi

Since you're in the EBI you will probably have more luck using the internal mirrors of ensembl databases. The kind of error you are seeing happens when you're either a long distance away from the server or the server you're querying is under excessive load. If you search confluence you should find the connection details 

Andy

Sent from my mobile.

> On 31 Oct 2014, at 09:57, Nathalie Conte <nconte at ebi.ac.uk> wrote:
> 
> 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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