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

[Janet Young]

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

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