[ensembl-dev] Variant Effect predictor error message

[Andreas Kusalananda Kähäri]

Hi Mark,

Sorry for not spotting your message until now.

Did you get the Ensembl Core API from the tar archive here?:
http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-64&view=tar
In that case, I don't know why you're seeing this problem unless
you're pointing the VEP at a server with no release 64 database on it.

Alternatively, if you have checked out the API through CVS, I'm
guessing that this is because you have checked out the HEAD revision
of the Ensembl Core API. This revision of the API will currently look
for release 65 databases on the server that you point it at
(ensembldb.ensembl.org, for example), but since these have not been
release yet it will fail to find any. In this case, try checking out
the 'branch-ensembl-64' branch instead.


That's my initial diagnosis.


AKK



On 25 October 2011 15:38, Mark Aquino <aquinom85 at me.com> wrote:
> Hi,
>
> I'm getting this error:
>
> homo_sapiens is not a valid species name for this instance
> homo_sapiens is not a valid species name for this instance
> Use of uninitialized value $species in hash element at /users/maquino/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 958.
> Use of uninitialized value $species in hash element at /users/maquino/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 969.
> ERROR: Could not connect to core database
>
> When I try to run the variant effect predictor.
>
> Is the core database still down and that's what's causing this error or is there something else going wrong here?
>
> -Mark
>
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-- 
Andreas Kusalananda Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom