<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello,<div><br></div><div><br></div><div><div>I'm doing : </div><div><br></div><div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); "><span style="color: rgb(178, 69, 243); "><span class="Apple-tab-span" style="white-space: pre; "> </span>my </span><span style="color: rgb(0, 0, 0); ">$</span><span style="color: rgb(178, 55, 243); ">registry</span><span style="color: rgb(0, 0, 0); "> </span><span style="color: rgb(193, 53, 0); ">= </span>'Bio::EnsEMBL::Registry'<span style="color: rgb(193, 53, 0); ">;</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span style="color: rgb(193, 53, 0); "><span class="Apple-tab-span" style="white-space: pre; "> </span></span>$<span style="color: rgb(178, 55, 243); ">registry</span><span style="color: rgb(193, 53, 0); ">-></span>load_registry_from_db<span style="color: rgb(193, 53, 0); ">(</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(194, 27, 45); "><span style="color: rgb(193, 53, 0); "> <span class="Apple-tab-span" style="white-space: pre; "> </span>-</span><span style="color: rgb(0, 0, 0); ">host </span><span style="color: rgb(193, 53, 0); ">=> </span><span style="color: rgb(4, 51, 255); ">'<a href="http://ensembldb.ensembl.org/">ensembldb.ensembl.org</a>'</span><span style="color: rgb(193, 53, 0); ">, </span># alternatively '<a href="http://useastdb.ensembl.org/">useastdb.ensembl.org</a>'</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "> <span class="Apple-tab-span" style="white-space: pre; "> </span><span style="color: rgb(193, 53, 0); ">-</span>user <span style="color: rgb(193, 53, 0); ">=> </span><span style="color: rgb(4, 51, 255); ">'anonymous'</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(4, 51, 255); "><span class="Apple-tab-span" style="white-space: pre; "> </span><span style="color: rgb(193, 53, 0); ">);</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; min-height: 15px; "><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(178, 55, 243); "><span style="color: rgb(193, 53, 0); "><span class="Apple-tab-span" style="white-space: pre; "> </span></span><span style="color: rgb(178, 69, 243); ">my </span><span style="color: rgb(0, 0, 0); ">$</span>gene_adaptor<span style="color: rgb(0, 0, 0); "> </span> <span style="color: rgb(193, 53, 0); ">= </span><span style="color: rgb(0, 0, 0); ">$</span>registry<span style="color: rgb(193, 53, 0); ">-></span><span style="color: rgb(0, 0, 0); ">get_adaptor</span><span style="color: rgb(193, 53, 0); ">( </span><span style="color: rgb(4, 51, 255); ">'Human'</span><span style="color: rgb(193, 53, 0); ">, </span><span style="color: rgb(4, 51, 255); ">'Core'</span><span style="color: rgb(193, 53, 0); ">, </span><span style="color: rgb(4, 51, 255); ">'Gene' </span><span style="color: rgb(193, 53, 0); ">);</span></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(194, 27, 45); "><span style="color: rgb(193, 53, 0); "><span class="Apple-tab-span" style="white-space: pre; "> </span></span>#COG6</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; "><span class="Apple-tab-span" style="white-space: pre; "> </span><span style="color: rgb(178, 69, 243); ">my </span>$<span style="color: rgb(178, 55, 243); ">gene</span> <span style="color: rgb(193, 53, 0); ">= </span>$<span style="color: rgb(178, 55, 243); ">gene_adaptor</span><span style="color: rgb(193, 53, 0); ">-></span>fetch_by_display_label<span style="color: rgb(193, 53, 0); ">(</span>$<span style="color: rgb(178, 55, 243); ">geneLabel</span><span style="color: rgb(193, 53, 0); ">);</span></div></div><div><br></div><div>$geneLabel = COG6</div><div><br></div><div>This was working fine last week up to Thursday afternoon but it's not working anymore. </div><div>I get the following message pasted below.</div><div><br></div><div>Would somebody be able to help me? :-)</div><div><br></div><div>Thanks for your help,</div><div>Catherine</div><div> </div><div><br></div><div><pre class="error">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, <a href="http://g.is/">g.is</a>_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 <a href="http://g.is/">g.is</a>_current = 1
': DBD::mysql::st execute failed: <b><span style="font-size: 14px; ">MySQL server has gone away at /data/perl5/lib/perl5/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 46</span>8</b>.
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
---------------------------------------------------</pre></div></div><div><br></div></body></html>