[ensembl-dev] Losing connection to MySQL for large queries

Will McLaren wm2 at ebi.ac.uk
Tue Oct 4 10:04:32 BST 2011


Hi Chris,

Try adding the following line to your code before you create the slice adaptor:

$registry->set_reconnect_when_lost();

Cheers

Will

On 4 October 2011 09:20, Chris Raistrick <chris.raistrick at bristol.ac.uk> wrote:
> Dear all,
>
> Getting an error when trying to retrieve a complete list of variant
> IDs via the ensembl variation database:
>
> [example std out]
> name = 'rs79594517', source = 'dbSNP', chr = '3'
> name = 'rs78223957', source = 'dbSNP', chr = '3'
> name = 'rs112696692', source = 'dbSNP', chr = '3'
> name = 'rs9761692', source = 'dbSNP', chr = '3'
> Chromosome 4
>        Connected to the Ensembl Registry
>        Slice adaptor generated
> DBD::mysql::st execute failed: Lost connection to MySQL server during
> query at .../ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line
> 287.
> DBD::mysql::st execute failed: Lost connection to MySQL server during
> query at .../ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line
> 287.
>
> Each time I start a new chromosome using this code:
>
>                print "Chromosome $chr\n";
>
>                # connect to Ensembl registry
>                my $registry = 'Bio::EnsEMBL::Registry';
>                $registry->load_registry_from_db(
>                    -host => 'ensembldb.ensembl.org',
>                    -user => 'anonymous'
>                );
>
>                # get slice for chromosome
>                my $slice_adaptor = $registry->get_adaptor('homo_sapiens', 'core', 'slice');
>                my $slice = $slice_adaptor->fetch_by_region('chromosome',$chr);
>
>                # get variations by slice
>                my $vf_adaptor = $registry->get_adaptor('homo_sapiens', 'variation',
> 'variationfeature');
>                my $vfs = $vf_adaptor->fetch_all_by_Slice($slice);
>
>                foreach my $vf (@{$vfs}){
>                                my $var_id = $vf->variation_name;
>                                ..
>
> I read the last few messages I could find related on here and they
> said this fix would be in by release 64 (I downloaded the modules last
> week, so assume I'm on 64).
>
> Please help, I've never had this problem using the Ensembl API (in 4 years).
>
> Chris
>
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