[ensembl-dev] compara: not a valid species name (check DB and API version)

[Stephen Fitzgerald]

Hi Janet, this is a registry issue. The latest database version on the 
host you specify (-host => 'mysql.ebi.ac.uk',) is 
'ensembl_compara_metazoa_23_76'. Your API checkout may be more recent

check using "git branch".


>cd ~/ensembl/
>git branch
   * master
   release/74
   release/75
   release/76
   release/77
>git checkout release/76
>git branch
   master
   release/74
   release/75
* release/76
   release/77

If you execute the above commands for both the "ensembl" and the 
"ensembl-compara" repositories and then run your script it should work.

Alternatively, you can disregard the above and specify the database 
version to use in the registry hash, like this:

Bio::EnsEMBL::Registry->load_registry_from_db(
  -host =>'mysql.ebi.ac.uk',
  -user =>"anonymous",
  -db_version=>76,
  -port =>4157);

This should also work, but you run the risk of API and database schema 
version incompatibilities at a later stage.


Hope this helps,
Stephen.



On Fri, 7 Nov 2014, Janet Young wrote:

> Hi there,
> I'm struggling a little with something pretty basic and and hoping for some help. I'm trying to follow instructions from here:
>     http://ensemblgenomes.org/info/access/api
> My goal later on is to download some protist sequences, but I'm struggling simply to implement the code exactly as it is given in the instructions above.
>  I'm not sure if there's an access problem with the database, or if the code no longer matches the tutorial web page above. 
> 
> My very short starter script is taken from the Compara section of that webpage (with a couple of print lines thrown in for troubleshooting purposes):
> 
> -----------
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> use Bio::EnsEMBL::Registry;
> 
> print "loading registry\n";
> Bio::EnsEMBL::Registry->load_registry_from_db(
>     -host => 'mysql.ebi.ac.uk',
>     -port => 4157);
> 
> print "getting adaptor\n";
> my $genome_db_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
>     'metazoa', 'compara', 'GenomeDB');
> -----------
> 
> Running the script, the registry seems to load OK, but I get this error upon getting the adaptor:
> 
> -------------------- WARNING ----------------------
> MSG: metazoa is not a valid species name (check DB and API version)
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1200
> CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 985
> Date (localtime)    = Fri Nov  7 17:02:18 2014
> Ensembl API version = 77
> ---------------------------------------------------
> 
> -------------------- EXCEPTION --------------------
> MSG: Can not find internal name for species 'metazoa'
> STACK Bio::EnsEMBL::Registry::get_adaptor /home/jayoung/malik_lab_shared/perl/ensembl/modules/Bio/EnsEMBL/Registry.pm:987
> STACK toplevel ./testEnsemblScript.bioperl:13
> Date (localtime)    = Fri Nov  7 17:02:18 2014
> Ensembl API version = 77
> ---------------------------------------------------
> 
> I updated my perl API this afternoon - same problem before and after updating.
> 
> On googling that error I did find an old post where there was a temporary permissions issue:
> http://article.gmane.org/gmane.science.biology.ensembl.devel/8637/match=can+not+find+internal+name+species+metazoa
> 
> Is something like that happening again?  (or, maybe I'm messing something up - it's been known!)
> 
> thanks very much,
> 
> Janet Young
> 
> ------------------------------------------------------------------- 
> 
> Dr. Janet Young 
> 
> Malik lab
> http://research.fhcrc.org/malik/en.html
> 
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., A2-025, 
> P.O. Box 19024, Seattle, WA 98109-1024, USA.
> 
> tel: (206) 667 4512
> email: jayoung  ...at...  fhcrc.org
> 
> ------------------------------------------------------------------- 
> 
> 
>