[ensembl-dev] VEP Conservation Plugin error
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Thu Oct 10 11:04:52 BST 2013
Hello Matthieu,
Indeed conservation score is appearing in output annotated file.
Thank you for the information, I was just wanted to be sure this wasn't
an error and just a warning.
Again thanks !
Best regards,
Guillermo.
On 10/10/2013 11:25 AM, Matthieu Muffato wrote:
> 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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