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

[Stephen Trevanion]

Hi Bob,

Sorry, missed this earlier. I've not come across the fix you've found, 
but the error message you see is indicative of a misconfiguration.

The entries for the alternative assembly in the configuration file 
should match that in the vega database:

$ grep ALTERNATIVE_ASSEMBLIES 
public-plugins/ensembl/conf/ini-files/Homo_sapiens.ini
ALTERNATIVE_ASSEMBLIES    = [ VEGA45 ]

use homo_sapiens_vega_65_37;
select * from coord_system where name = 'chromosome' and version like 
'VEGA%';
+-----------------+------------+------------+---------+------+-----------------+
| coord_system_id | species_id | name       | version | rank | 
attrib          |
+-----------------+------------+------------+---------+------+-----------------+
|           10001 |          1 | chromosome | VEGA45  |  101 | 
default_version |
+-----------------+------------+------------+---------+------+-----------------+

The error message you get can arise because there is a mismatch between 
the two - are you using 64 databases with a 65 API ?

The above applies to mouse and zebrafish as well.

Regards,

Steve


On 02/22/12 12:30, Bob Briscoe wrote:
> OK, I've found a work around, which involves capitalising the 
> chromosome name, i.e. the following works:
>
> http://ourserver/Homo_sapiens/Gene/Summary?db=VEGA;g=OTTHUMG00000017411;r=13:32889611-32973347
>
> 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.
>
> Bob
>
> *From:* Bob Briscoe <paw_deer at yahoo.co.uk>
> *To:* "dev at ensembl.org" <dev at ensembl.org>
> *Sent:* Tuesday, 21 February 2012, 8:04
> *Subject:* [ensembl-dev] Runtime Error in component 
> "EnsEMBL::Web::Component::Gene::Summary [content]"
>
> 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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