[ensembl-dev] VEP Conservation Plugin error

[Guillermo Marco Puche]

Hello Will,

I'm testing it with example.vcf included in vep73 package.

This is the command i'm using:

*./variant_effect_predictor.pl -i example.vcf -o example.vep 
-dir_plugins /home/likewise-open/SGNET/gmarco/vep_config/Plugins -plugin 
Conservation --database --force_overwrite*


I've installed bioperl, ensembl core, compara, variation, functgenomics 
& ontology api (downloaded this morning).

It's strange because indeed output file has conservation score in 
output. I don't know what all those errors come from.


Best regards,
Guillermo.

On 10/07/2013 04:29 PM, Will McLaren wrote:
> Hello,
>
> I don't see any similar issues testing with a small input file.
>
> The Conservation plugin depends on the ensembl-compara API module - 
> check that you have updated it to the latest version (73). Note that 
> this is not done by the VEP installer since the ensembl-compara module 
> is not required by the core VEP.
>
> If you're using CVS, just do:
>
> cd /home/likewise-open/SGNET/gmarco/src/ensembl-compara/
> cvs up -dPr branch-ensembl-73
>
> If you still see the issue, can you please provide a sample of input 
> and the command line flags you were using that recreates the error.
>
> Thanks
>
> Will McLaren
> Ensembl Variation
>
>
>
> On 7 October 2013 11:54, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     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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