[ensembl-dev] VEP Conservation Plugin error

[James Walker]

Hello Will,

I'm using vep cache plus local ensembl database to annotate variants.

I don't really understand what do you refer with: "Is there any chance you
have accidentally checked out head code (instead of branch 73) for the
ensembl-compara API?"

I've modified code in the script from:

sub version {
    return '2.3';
}

to

sub version {
    return '73';
}

Regards,
James.



2013/10/14 Will McLaren <wm2 at ebi.ac.uk>

> Hi James, Guillermo,
>
> We're struggling to recreate the problem at our end.
>
> While we do still see the warning message (which will disappear in 74 as
> Matthieu says), the plugin seems to be working fine.
>
> I've tested it on the example.vcf supplied with the VEP and a larger set
> of ~3500 exonic variants from the 1000 genomes project, and I see
> Conservation scores in the output for every variant in my test set.
>
> Are you seeing any other error messages? Are you using a local database
> copy, or relying on the ensembldb connection (the default when using VEP)?
>
> Is there any chance you have accidentally checked out head code (instead
> of branch 73) for the ensembl-compara API?
>
> MethodLinkSpeciesSet is not deprecated, although a couple of deprecated
> methods in it were removed in 73, though these are not used by the plugin.
>
> Some more information would be useful!
>
> Thanks
>
> Will
>
>
> On 14 October 2013 15:10, James Walker <walker.james.kerrigan at gmail.com>wrote:
>
>> I'm experiencing the exact same problem. Plugin seems to be broken.
>>
>>
>> James.
>>
>>
>> _______________________________________________
>> 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/20131014/941eb792/attachment.html>