[ensembl-dev] VEP Conservation Plugin error

[Will McLaren]

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/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20131014/672359f6/attachment.html>