[ensembl-dev] VEP Conservation Plugin error
Matthieu Muffato
muffato at ebi.ac.uk
Thu Oct 10 10:25:39 BST 2013
Hi Guillermo,
The message "Cannot find the core database of '...' in the Registry. Be
aware that getting Core objects from Compara is not possible for this
species" is not an error, but just a warning issued by the Compara API.
I think it is still fine in your case (getting conservation scores).
There could only be a problem if you have a script that tries to get a
Slice, Gene, Transcript object from a Compara alignment, gene tree, etc
The code in e73 is systematically showing those warnings, whilst the
previous versions did not at all. It will be less verbose again in e74.
Best,
Matthieu
On 10/10/13 09:19, Guillermo Marco Puche wrote:
> Hello Will,
>
> I've reinstalled the whole API and I'm still getting the same errors.
> I'm testing it with remote ensembl installation to discard there's a
> problem with my own DB. In fact I still get the same error. I'm using
> example.vcf file provided with vep as input.
>
> I attach a log in this e-mail with the vep command (same I posted in my
> previous e-mail) and the whole output.
>
> Thank you !
>
> Best regards,
> Guillermo.
>
>
> On 10/07/2013 05:02 PM, Guillermo Marco Puche wrote:
>> 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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--
Matthieu Muffato, Ph.D.
Ensembl Developer and Ensembl Compara Manager
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
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