[ensembl-dev] VEP Conservation Plugin error
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Fri Oct 11 09:02:47 BST 2013
Hello Matthieu,
I've been using VEP overnight with a more extense dataset. I've
annotated more than 40k variants and conservation score is being always
reported as empty ("-")
Currently the "script" I'm using is Conservation.pm plugin provided in
VEP repository:
https://github.com/ensembl-variation/VEP_plugins/blob/master/Conservation.pm
Only problem I see is use of MethodLinkSpeciesSet which is deprecated in
current version.
On 10/10/2013 12:04 PM, Guillermo Marco Puche wrote:
> 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.
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing listDev at ensembl.org
>>>>> Posting guidelines and subscribe/unsubscribe
>>>>> info:http://lists.ensembl.org/mailman/listinfo/dev
>>>>> Ensembl Blog:http://www.ensembl.info/
>>>>
>>>>
>>>> _______________________________________________
>>>> Dev mailing listDev at ensembl.org
>>>> Posting guidelines and subscribe/unsubscribe
>>>> info:http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog:http://www.ensembl.info/
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20131011/ebea2a57/attachment.html>
More information about the Dev
mailing list