[ensembl-dev] core api : MySQL server has gone away

Tue Dec 3 11:19:33 GMT 2013

Hello,

I'm doing : 

	my $registry = 'Bio::EnsEMBL::Registry';

	$registry->load_registry_from_db(
    		-host => 'ensembldb.ensembl.org', # alternatively 'useastdb.ensembl.org'
    		-user => 'anonymous'
		);

			my $gene_adaptor  = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
			#COG6
			my $gene = $gene_adaptor->fetch_by_display_label($geneLabel);

$geneLabel = COG6

This was working fine last week up to Thursday afternoon but it's not working anymore. 
I get the following message pasted below.

Would somebody be able to help me? :-)

Thanks for your help,
Catherine

MSG: Detected an error whilst executing SQL 'SELECT  g.gene_id, g.seq_region_id, g.seq_region_start, g.seq_region_end, g.seq_region_strand, g.analysis_id, g.biotype, g.display_xref_id, g.description, g.status, g.source, g.is_current, g.canonical_transcript_id, g.canonical_annotation, g.stable_id, g.version, UNIX_TIMESTAMP(g.created_date), UNIX_TIMESTAMP(g.modified_date), x.display_label, x.dbprimary_acc, x.description, x.version, exdb.db_name, exdb.status, exdb.db_release, exdb.db_display_name, x.info_type, x.info_text 
FROM (( (gene g) 
  LEFT JOIN xref x ON x.xref_id = g.display_xref_id ) 
  LEFT JOIN external_db exdb ON exdb.external_db_id = x.external_db_id ) 
 WHERE x.display_label = ? AND g.is_current = 1 
': DBD::mysql::st execute failed: MySQL server has gone away at /data/perl5/lib/perl5/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 468.

STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch /data/perl5/lib/perl5/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:469
STACK Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_by_display_label /data/perl5/lib/perl5/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm:173
STACK Cnv::SampleSelection::SampleSelection::__ANON__[/data/www/cl6/Cnv/lib/Cnv/SampleSelection/SampleSelection.pm:256] /data/www/cl6/Cnv/lib/Cnv/SampleSelection/SampleSelection.pm:118
STACK Dancer::Route::execute /data/perl5/lib/perl5/Dancer/Route.pm:274
STACK Dancer::Route::__ANON__ /data/perl5/lib/perl5/Dancer/Route.pm:177
STACK (eval) /usr/share/perl5/Try/Tiny.pm:71
STACK Try::Tiny::try /usr/share/perl5/Try/Tiny.pm:67
STACK Dancer::Route::run /data/perl5/lib/perl5/Dancer/Route.pm:191
STACK Dancer::Renderer::__ANON__ /data/perl5/lib/perl5/Dancer/Renderer.pm:134
STACK (eval) /usr/share/perl5/Try/Tiny.pm:76
STACK Try::Tiny::try /usr/share/perl5/Try/Tiny.pm:67
STACK Dancer::Renderer::get_action_response /data/perl5/lib/perl5/Dancer/Renderer.pm:143
STACK Dancer::Renderer::render_action /data/perl5/lib/perl5/Dancer/Renderer.pm:31
STACK Dancer::Handler::__ANON__ /data/perl5/lib/perl5/Dancer/Handler.pm:84
STACK (eval) /usr/share/perl5/Try/Tiny.pm:71
STACK Try::Tiny::try /usr/share/perl5/Try/Tiny.pm:67
STACK Dancer::Handler::render_request /data/perl5/lib/perl5/Dancer/Handler.pm:113
STACK Dancer::Handler::handle_request /data/perl5/lib/perl5/Dancer/Handler.pm:76
STACK Dancer::_start /data/perl5/lib/perl5/Dancer.pm:470
STACK Plack::Sandbox::_2fdata_2fwww_2fcl6_2fCnv_2fapp_2epsgi::__ANON__ /data/www/cl6/Cnv/app.psgi:18
STACK Plack::App::URLMap::call /data/perl5/lib/perl5/Plack/App/URLMap.pm:71
STACK Plack::Component::__ANON__ /data/perl5/lib/perl5/Plack/Component.pm:39
STACK Plack::Middleware::Assets::call /data/perl5/lib/perl5/Plack/Middleware/Assets.pm:97
STACK Plack::Component::__ANON__ /data/perl5/lib/perl5/Plack/Component.pm:39
STACK Plack::Middleware::Assets::call /data/perl5/lib/perl5/Plack/Middleware/Assets.pm:97
STACK Plack::Component::__ANON__ /data/perl5/lib/perl5/Plack/Component.pm:39
STACK Plack::Middleware::Assets::call /data/perl5/lib/perl5/Plack/Middleware/Assets.pm:97
STACK Plack::Component::__ANON__ /data/perl5/lib/perl5/Plack/Component.pm:39
STACK Plack::Middleware::Assets::call /data/perl5/lib/perl5/Plack/Middleware/Assets.pm:97
STACK Plack::Component::__ANON__ /data/perl5/lib/perl5/Plack/Component.pm:39
STACK Plack::Middleware::Lint::call /data/perl5/lib/perl5/Plack/Middleware/Lint.pm:24
STACK Plack::Component::__ANON__ /data/perl5/lib/perl5/Plack/Component.pm:39
STACK Plack::Middleware::StackTrace::__ANON__ /data/perl5/lib/perl5/Plack/Middleware/StackTrace.pm:31
STACK (eval) /usr/share/perl5/Try/Tiny.pm:71
STACK Try::Tiny::try /usr/share/perl5/Try/Tiny.pm:67
STACK Plack::Middleware::StackTrace::call /data/perl5/lib/perl5/Plack/Middleware/StackTrace.pm:35
STACK Plack::Component::__ANON__ /data/perl5/lib/perl5/Plack/Component.pm:39
STACK Plack::Middleware::AccessLog::call /data/perl5/lib/perl5/Plack/Middleware/AccessLog.pm:29
STACK Plack::Component::__ANON__ /data/perl5/lib/perl5/Plack/Component.pm:39
STACK (eval) /data/perl5/lib/perl5/Plack/Util.pm:143
STACK Plack::Util::run_app /data/perl5/lib/perl5/Plack/Util.pm:143
STACK Starman::Server::process_request /data/perl5/lib/perl5/Starman/Server.pm:256
STACK Net::Server::run_client_connection /data/perl5/lib/perl5/Net/Server.pm:75
STACK (eval) /data/perl5/lib/perl5/Net/Server/PreFork.pm:229
STACK Net::Server::PreFork::run_child /data/perl5/lib/perl5/Net/Server/PreFork.pm:229
STACK Net::Server::PreFork::run_n_children /data/perl5/lib/perl5/Net/Server/PreFork.pm:187
STACK Net::Server::PreFork::loop /data/perl5/lib/perl5/Net/Server/PreFork.pm:111
STACK Net::Server::run /data/perl5/lib/perl5/Net/Server.pm:61
STACK Starman::Server::run /data/perl5/lib/perl5/Starman/Server.pm:67
STACK Plack::Handler::Starman::run /data/perl5/lib/perl5/Plack/Handler/Starman.pm:18
STACK Plack::Loader::Delayed::run /data/perl5/lib/perl5/Plack/Loader/Delayed.pm:20
STACK Plack::Runner::run /data/perl5/lib/perl5/Plack/Runner.pm:277
STACK toplevel /data/perl5/bin/starman:41
Date (localtime)    = Tue Dec  3 10:28:46 2013
Ensembl API version = 73
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