[ensembl-dev] Ensembl API Version 72: Supported Species

[Andy Yates]

Hi there

This normally means the registry has been unable to load the tomato database from the database server. If you run the loading code with a -VERBOSE flag it will give you a bit more information about what it's loading. Are you trying to load the species from ensembl genomes' public service or from a local copy?

Andy

Sent from my mobile.

On 7 Sep 2013, at 02:04, Alexander Pico <apico at gladstone.ucsf.edu> wrote:

> I'm receiving an error for just 2 species (out of list of 31) against version 72 of your Perl API:
> * Solanum lycopersicum
> * Glycine Max
> 
> Here's an example:
> 
> -------------------- WARNING ----------------------
> MSG: Solanum lycopersicum is not a valid species name (check DB and API version)
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1188
> CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 973
> Date (localtime)    = Fri Sep  6 17:14:51 2013
> Ensembl API version = 72
> ---------------------------------------------------
> 
> -------------------- EXCEPTION --------------------
> MSG: Can not find internal name for species 'Solanum lycopersicum'
> STACK Bio::EnsEMBL::Registry::get_adaptor /***/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:975
> STACK toplevel Ensembl_ETL_Device_v18_local.pl:437
> Date (localtime)    = Fri Sep  6 17:14:51 2013
> Ensembl API version = 72
> ---------------------------------------------------
> 
> I know these worked in earlier API versions. Any guesses?
> - Alex
> 
> 
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