[ensembl-dev] Runtime Error in component "EnsEMBL::Web::Component::Gene::Summary [content]"
Bob Briscoe
paw_deer at yahoo.co.uk
Wed Feb 22 13:58:54 GMT 2012
Hi Stephen,
All seems fine when I run your diagnostics:
$ grep ALTERNATIVE_ASSEMBLIES public-plugins/ensembl/conf/ini-files/Homo_sapiens.ini
ALTERNATIVE_ASSEMBLIES = [ VEGA45 ]
$ mysql -u root -p*********
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 9574
Server version: 5.0.77 Source distribution
Type 'help;' or '\h' for help. Type '\c' to clear the buffer.
mysql> use homo_sapiens_vega_65_37;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Database changed
mysql> 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 |
+-----------------+------------+------------+---------+------+-----------------+
1 row in set (0.01 sec)
It all seems like your output, but thanks for the interest in the problem.
Best,
Bob
________________________________
From: Stephen Trevanion <st3 at sanger.ac.uk>
To: Bob Briscoe <paw_deer at yahoo.co.uk>; Ensembl developers list <dev at ensembl.org>
Sent: Wednesday, 22 February 2012, 13:18
Subject: Re: [ensembl-dev] Runtime Error in component "EnsEMBL::Web::Component::Gene::Summary [content]"
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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