<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>OK, I've found a work around, which involves capitalising the chromosome name, i.e. the following works:</span></div><div><br>http://ourserver/Homo_sapiens/Gene/Summary?db=VEGA;g=OTTHUMG00000017411;r=13:32889611-32973347</div><div><br><span></span></div>I'm at a loss to explain why this API version (65) under Red Hat 5 needs the capitilisation whereas API version (64) under Ubuntu didn't, but I suppose I can live with this.<br><br>Bob<br><br><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Bob Briscoe <paw_deer@yahoo.co.uk><br> <b><span style="font-weight: bold;">To:</span></b> "dev@ensembl.org"
<dev@ensembl.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Tuesday, 21 February 2012, 8:04<br> <b><span style="font-weight: bold;">Subject:</span></b> [ensembl-dev] Runtime Error in component "EnsEMBL::Web::Component::Gene::Summary [content]"<br> </font> </div> <br><div id="yiv1841225282"><div><div style="color:#000;background-color:#fff;font-family:arial, helvetica, sans-serif;font-size:12pt;"><div>Hi All,</div><div>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:</div><div><br></div><div>http://ourserver/Homo_sapiens/Gene/Summary?db=vega;g=OTTHUMG00000017411;r=13:32889611-32973347</div><div><br></div><div>The first part of the result reports the error:</div><div class="yiv1841225282nav-heading">
<h1 style="font-weight:normal;" class="yiv1841225282summary-heading"><font size="3">Gene: BRCA2 <span class="yiv1841225282summary-subhead">OTTHUMG00000017411</span></font></h1>
</div>
<div class="yiv1841225282content"><h4>Runtime Error in component "<b>EnsEMBL::Web::Component::Gene::Summary</b> [content]"</h4><div>Function <b>EnsEMBL::Web::Component::Gene::Summary</b> fails to execute due to the following error:</div>
<pre class="yiv1841225282syntax-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
---------------------------------------------------
<br>The second part of the output, the graphical Gene summary, works just fine. Also, the same query <br>on an earlier installation, of version 64 of Ensembl but under Ubuntu 10.04, works just fine <br>throughout.<br><br>Any clues/hints on how to fix this will be much appreciated.<br><br>Thx,<br>Bob<br></pre></div></div></div></div><br>_______________________________________________<br>Dev mailing list <a ymailto="mailto:Dev@ensembl.org" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br><br><br> </div> </div> </div></body></html>