[ensembl-dev] Runtime Error in component "EnsEMBL::Web::Component::Gene::Summary [content]"

Bob Briscoe paw_deer at yahoo.co.uk
Tue Feb 21 08:04:59 GMT 2012


Hi All,
As still a relative newbie at setting up Ensembl resources I'd be grateful with help with an error I'm getting to the following query to an installation on version 65 of Ensembl under Redhat 5:

http://ourserver/Homo_sapiens/Gene/Summary?db=vega;g=OTTHUMG00000017411;r=13:32889611-32973347

The first part of the result reports the error:
Gene: BRCA2 OTTHUMG00000017411
Runtime Error in component "EnsEMBL::Web::Component::Gene::Summary [content]"
Function EnsEMBL::Web::Component::Gene::Summary fails to execute due to the following error:
-------------------- EXCEPTION -------------------- MSG: Cannot project to unknown coordinate system [chromosome VEGA44] STACK Bio::EnsEMBL::Slice::project /usr/local/ensembl/ensembl/modules/Bio/EnsEMBL/Slice.pm:840 STACK EnsEMBL::Web::Object::Gene::vega_projection /usr/local/ensembl/modules/EnsEMBL/Web/Object/Gene.pm:1178 STACK EnsEMBL::Web::Component::transcript_table /usr/local/ensembl/modules/EnsEMBL/Web/Component.pm:750 STACK EnsEMBL::Web::Component::Gene::Summary::content ... /usr/local/ensembl/modules/EnsEMBL/Web/Component/Gene/Summary.pm:24 STACK EnsEMBL::Web::Component::get_content /usr/local/ensembl/modules/EnsEMBL/Web/Component.pm:137 STACK (eval) /usr/local/ensembl/modules/EnsEMBL/Web/Document/Panel.pm:415 STACK EnsEMBL::Web::Document::Panel::component_content ... /usr/local/ensembl/modules/EnsEMBL/Web/Document/Panel.pm:412 STACK EnsEMBL::Web::Document::Panel::content /usr/local/ensembl/modules/EnsEMBL/Web/Document/Panel.pm:316 STACK
 EnsEMBL::Web::Document::Element::Content::content ... /usr/local/ensembl/modules/EnsEMBL/Web/Document/Element/Content.pm:127 STACK EnsEMBL::Web::Controller::render_page /usr/local/ensembl/modules/EnsEMBL/Web/Controller.pm:220 STACK EnsEMBL::Web::Controller::Page::render_page /usr/local/ensembl/modules/EnsEMBL/Web/Controller/Page.pm:50 STACK EnsEMBL::Web::Controller::Page::init /usr/local/ensembl/modules/EnsEMBL/Web/Controller/Page.pm:37 STACK EnsEMBL::Web::Controller::new /usr/local/ensembl/modules/EnsEMBL/Web/Controller.pm:91 STACK EnsEMBL::Web::Apache::SpeciesHandler::handler_species ... /usr/local/ensembl/modules/EnsEMBL/Web/Apache/SpeciesHandler.pm:91 STACK EnsEMBL::Web::Apache::Handlers::handler /usr/local/ensembl/modules/EnsEMBL/Web/Apache/Handlers.pm:401 STACK (eval) -e:0 STACK toplevel -e:0 Ensembl API version = 65 --------------------------------------------------- 
The second part of the output, the graphical Gene summary, works just fine. Also, the same query 
on an earlier installation, of version 64 of Ensembl but under Ubuntu 10.04, works just fine 
throughout.

Any clues/hints on how to fix this will be much appreciated.

Thx,
Bob
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