[ensembl-dev] Variant Effect predictor error message

Will McLaren wm2 at ebi.ac.uk
Wed Oct 26 13:22:49 BST 2011


Hi Mark,

If you're using the public Ensembl DBs, the default port for
ensembldb.ensembl.org is 5306, not 3306.

This might be your problem.

Will

On 26 October 2011 13:17, Mark Aquino <aquinom85 at me.com> wrote:
> 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
>>>>
>>>> _______________________________________________
>>>> Dev mailing list    Dev at ensembl.org
>>>> List admin (including subscribe/unsubscribe):
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> List admin (including subscribe/unsubscribe):
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>




More information about the Dev mailing list