[ensembl-dev] Variant Effect predictor error message

[Mark Aquino]

Luca--

That's actually the first thing I tried but the error just changed to "human" is not a valid species name for this instance. 

Will -- 

I'll have to go back and double check this but I was using the ensembl and endembl variation APIs and bioperl1.2.3 all from the Ensembl downloads page that essentially lists "pre-requisite files" for the VEP (Redownloaded yesterday so whatever is most up to date via those links) Could be a versioning conflict with bioperl since 1.2.3 is quite old isn't it on 1.6+ now?

I was receiving this error while connecting (trying to) to the ensembl databases rather than my local db since I haven't had time to update them yet. Was using only sift/pph2/condel, format vcf, --no-whole-genome, and a port flag (3306).  

Intermediately, as a quick-fix, I just ran my files using vep2.0, the older APIs I had from before, and my locally installed Ensembl database. 


PS. On updating the databases locally is there a smarter way to do this than deleting the entire previous build and reloading the new schema and reinserting all the tables fresh, as this is what I have been doing. 

Sent from my iPhone

On Oct 26, 2011, at 4:52 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Mark,
> 
> Are you using the cache or connecting to the database?
> 
> In either case, is your API up to date and/or in sync with the version
> number of the database/cache you are using?
> 
> Will
> 
> On 26 October 2011 08:51, Venturini Luca <vntlcu41 at univr.it> wrote:
>> I would try using "human" as a species name, usually that functions. Also,
>> set the verbose flag - if the connection to the database functions, you
>> should see a list of all available species/dataset loaded from MySQL.
>> 
>> - Luca
>> 
>> 
>> Il 25/10/2011 16:38, Mark Aquino ha scritto:
>>> 
>>> 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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>> 
>> 
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