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

Tue Dec 3 11:37:58 GMT 2013

apologies, that was meant for Catherine only

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

kr2 at sanger.ac.uk
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 3 Dec 2013, at 11:37, Keiran Raine <kr2 at sanger.ac.uk> wrote:

> http://cgp-gbrowse-live.internal.sanger.ac.uk:8080/fast/gbrowse_details/prod_p2?name=BRCA2;class=Sequence;db_id=REFSEQ%3Adatabase
> 
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
> 
> kr2 at sanger.ac.uk
> Tel:+44 (0)1223 834244 Ext: 7703
> Office: H104
> 
> On 3 Dec 2013, at 11:19, Catherine Leroy <cl6 at sanger.ac.uk> wrote:
> 
>> 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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> 
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