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

[James Allen]

Hello,
Further to Stephen's explanation, an explanation of why there is no version 77 Ensembl Genomes database: There is usually a lag of 1-2 weeks between Ensembl and EG releases, but it's been longer than that this time due to a datacenter move than fell right in the middle of the projects' release dates. However, EG release 24 (i.e. the one that uses the Ensembl 77 schema/code) is scheduled for tomorrow (11th Nov), so you could wait till then, or use release 76 in the meantime.

Cheers,
James


On Mon, 10 Nov 2014 15:52:35 +0000 (GMT)
Stephen Fitzgerald <stephenf at ebi.ac.uk> wrote:

> 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
> > 
> > ------------------------------------------------------------------- 
> > 
> > 
> >