[ensembl-dev] VEP Conservation Plugin error

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Mon Oct 7 11:54:49 BST 2013


Hello,

I recently updated to ensembl73 database. I've found the following 
problem with Conservation plugin:

Cannot find the core database of 'takifugu_rubripes' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.

Cannot find the core database of 'ciona_savignyi' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.

Cannot find the core database of 'macaca_mulatta' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.

Cannot find the core database of 'echinops_telfairi' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.

Cannot find the core database of 'gasterosteus_aculeatus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /home/likewise-open/SGNET/gmarco/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.

(...)

-------------------- WARNING ----------------------

MSG: Unable to find method_link_species_set with method_link_type of Conservation_score and species_set_tag value of mammals

FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 567

CALLED BY: vep_config/Plugins/Conservation.pm  LINE: 82

Date (localtime)    = Mon Oct  7 12:36:33 2013

Ensembl API version = 73

---------------------------------------------------

2013-10-07 12:36:33 - Failed to instantiate plugin Conservation: Failed to fetch MLSS for Conservation_score and mammals


Thank you.

Best regards,
Guillermo.
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