[ensembl-dev] regulation feature error

[Nathan Johnson]

Hi

The error here details access to the flat files which support the  
signal tracks in the regulation displays. I suspect you have not set  
the following variable in your DEFAULTS.ini:

ENSEMBL_REGULATION_FILE_PATH

In here you should have the collection or 'col' files/dirs defined in  
the dbfile_registry table, which are available via the ftp site:

ftp://ftp.ensembl.org/pub/release-66/data_files/

Just the human and mouse files are required for the regulation  
displays, the chimp files support an rnaseq view.

Hope this help

Nath



On 31 Mar 2012, at 13:05, 陈岗 wrote:

> Hi All
>
> My Ensembl mirror has a error on the regulation feature page, the  
> error message is:
>
> AJAX error - Runtime Error in component  
> "EnsEMBL::Web::Component::Regulation::FeaturesByCellLine [content]"
>
> Function EnsEMBL::Web::Component::Regulation::FeaturesByCellLine  
> fails to execute due to the following error:
>
> 	-------------------- EXCEPTION --------------------
> 	MSG: Failed to open:
> 	... /homo_sapiens_funcgen_66_37//result_feature/ 
> GM12878_DNase1_ENCODE_Uw/result_features.GM12878_DNase1_ENCODE_
> 	... Uw.65.col
> 	No such file or directory
>
> 	STACK Bio::EnsEMBL::DBFile::FileAdaptor::open_file
> 	... /usr/local/Ensembl/ensembl/modules/Bio/EnsEMBL/DBFile/ 
> FileAdaptor.pm:146
> 	STACK Bio::EnsEMBL::DBFile::FileAdaptor::get_filehandle
> 	... /usr/local/Ensembl/ensembl/modules/Bio/EnsEMBL/DBFile/ 
> FileAdaptor.pm:80
> 	STACK Bio::EnsEMBL::DBFile::CollectionAdaptor::read_collection_blob
> 	... /usr/local/Ensembl/ensembl/modules/Bio/EnsEMBL/DBFile/ 
> CollectionAdaptor.pm:188
> 	STACK  
> Bio 
> ::EnsEMBL 
> ::Funcgen 
> ::DBSQL::ResultFeatureAdaptor::_fetch_from_file_by_Slice_ResultSet
> 	... /usr/local/Ensembl/ensembl-functgenomics/modules/Bio/EnsEMBL/ 
> Funcgen/DBSQL/ResultFeatureAdaptor.pm:800
> 	STACK  
> Bio 
> ::EnsEMBL 
> ::Funcgen::DBSQL::ResultFeatureAdaptor::fetch_all_by_Slice_ResultSets
> 	... /usr/local/Ensembl/ensembl-functgenomics/modules/Bio/EnsEMBL/ 
> Funcgen/DBSQL/ResultFeatureAdaptor.pm:743
> 	STACK EnsEMBL::Web::Object::Slice::get_data /usr/local/Ensembl/ 
> modules/EnsEMBL/Web/Object/Slice.pm:320
> 	STACK EnsEMBL::Web::Object::Slice::get_cell_line_data
> 	... /usr/local/Ensembl/modules/EnsEMBL/Web/Object/Slice.pm:221
> 	STACK  
> EnsEMBL::Web::Component::Regulation::FeaturesByCellLine::content
> 	... /usr/local/Ensembl/modules/EnsEMBL/Web/Component/Regulation/ 
> FeaturesByCellLine.pm:49
> 	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::Ajax::content
> 	... /usr/local/Ensembl/modules/EnsEMBL/Web/Document/Panel/Ajax.pm:9
> 	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::Component::init
> 	... /usr/local/Ensembl/modules/EnsEMBL/Web/Controller/Component.pm:47
> 	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 = 66
>
> How to fix it ?
>
> Thanks million
>
> -- 
> Gang Chen
> TILSI
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu  
> Province, P.R.China
> Phone:（+86）512-82782588
>
> _______________________________________________
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