[ensembl-dev] data importing and Genomic alignments errors

[陈岗]

Hi All

1.
EnsembkGenomes data importing has an error.

analysis_ctrl_rule.txt
analysis_data.txt
analysis_stats.txt
analysis_stats_monitor.txt
dataflow_rule.txt

above 5 text files exist in ensembl_compara_pan_homology_17_70 folder, but
ensembl_compara_pan_homology_17_70.sql doesn't contain the related table
creating commands.

either these files are redundent or the sql is wrong, Please check it.

2.
Genomic alignments (image) error on our local mirror.

On gene page, some alignments set work vrey well, but some of them doesn't,
such as alignment: Caenorhabditis brenneri-lastz.

The error message is:

AJAX error - Runtime Error in component
"EnsEMBL::Web::Component::Gene::Compara_AlignSliceBottom [content]"

Function EnsEMBL::Web::Component::Gene::Compara_AlignSliceBottom fails to
execute due to the following error:


-------------------- EXCEPTION --------------------
MSG: [] is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
STACK
Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::fetch_by_Slice_MethodLinkSpeciesSet
...
/usr/local/ensembl_metazoa/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/AlignSliceAdaptor.pm:119
STACK EnsEMBL::Web::Component::Compara_Alignments::get_alignments
...
/usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Component/Compara_Alignments.pm:198
STACK EnsEMBL::Web::Component::Compara_Alignments::get_slices
...
/usr/local/ensembl_metazoa/eg-plugins/common/modules/EnsEMBL/Web/Component/Compara_Alignments.pm:329
STACK EnsEMBL::Web::Component::Gene::Compara_AlignSliceBottom::content
...
/usr/local/ensembl_metazoa/eg-plugins/common/modules/EnsEMBL/Web/Component/Gene/Compara_AlignSliceBottom.pm
... :55
STACK EnsEMBL::Web::Component::get_content
/usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Component.pm:139
STACK (eval)
/usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Document/Panel.pm:400
STACK EnsEMBL::Web::Document::Panel::component_content
... /usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Document/Panel.pm:397
STACK EnsEMBL::Web::Document::Panel::Ajax::content
... /usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Document/Panel/Ajax.pm:9
STACK EnsEMBL::Web::Document::Element::Content::content
...
/usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Document/Element/Content.pm:127
STACK EnsEMBL::Web::Controller::render_page
/usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Controller.pm:218
STACK EnsEMBL::Web::Controller::Component::init
...
/usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Controller/Component.pm:45
STACK EnsEMBL::Web::Controller::new
/usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Controller.pm:90
STACK EnsEMBL::Web::Apache::SpeciesHandler::handler_species
...
/usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Apache/SpeciesHandler.pm:91
STACK EnsEMBL::Web::Apache::Handlers::handler
... /usr/local/ensembl_metazoa/modules/EnsEMBL/Web/Apache/Handlers.pm:369
STACK (eval) -e:0
STACK toplevel -e:0
Date (localtime)    = Sun Feb 17 13:54:05 2013
Ensembl API version = 70

How to fix it?

Thanks
-- 
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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