<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi there,<div><br></div><div>I'm struggling a little with something pretty basic and and hoping for some help. I'm trying to follow instructions from here:</div><div> <a href="http://ensemblgenomes.org/info/access/api">http://ensemblgenomes.org/info/access/api</a></div><div>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. </div><div><br></div><div>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):</div><div><br></div><div>-----------</div><div><div>#!/usr/bin/perl</div><div><br></div><div>use strict;</div><div>use warnings;</div><div>use Bio::EnsEMBL::Registry;</div><div><br></div><div>print "loading registry\n";</div><div>Bio::EnsEMBL::Registry->load_registry_from_db(</div><div> -host => '<a href="http://mysql.ebi.ac.uk">mysql.ebi.ac.uk</a>',</div><div> -port => 4157);</div><div><br></div><div>print "getting adaptor\n";</div><div>my $genome_db_adaptor = Bio::EnsEMBL::Registry->get_adaptor(</div><div> 'metazoa', 'compara', 'GenomeDB');</div></div><div>-----------</div><div><br></div><div>Running the script, the registry seems to load OK, but I get this error upon getting the adaptor:</div><div><div style="margin: 0px; font-size: 13px; min-height: 15px;"><br></div><div style="margin: 0px; font-size: 13px;"><div style="margin: 0px;">-------------------- WARNING ----------------------</div><div style="margin: 0px;">MSG: metazoa is not a valid species name (check DB and API version)</div><div style="margin: 0px;">FILE: Bio/EnsEMBL/Registry.pm LINE: 1200</div><div style="margin: 0px;">CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 985</div><div style="margin: 0px;">Date (localtime) = Fri Nov 7 17:02:18 2014</div><div style="margin: 0px;">Ensembl API version = 77</div><div style="margin: 0px;">---------------------------------------------------</div><div style="margin: 0px; min-height: 15px;"><br></div><div style="margin: 0px;">-------------------- EXCEPTION --------------------</div><div style="margin: 0px;">MSG: Can not find internal name for species 'metazoa'</div><div style="margin: 0px;">STACK Bio::EnsEMBL::Registry::get_adaptor /home/jayoung/malik_lab_shared/perl/ensembl/modules/Bio/EnsEMBL/Registry.pm:987</div><div style="margin: 0px;">STACK toplevel ./testEnsemblScript.bioperl:13</div><div style="margin: 0px;">Date (localtime) = Fri Nov 7 17:02:18 2014</div><div style="margin: 0px;">Ensembl API version = 77</div><div style="margin: 0px;">---------------------------------------------------</div><div><br></div><div><span style="font-size: 12px;">I updated my perl API this afternoon - same problem before and after updating.</span></div><div><span style="font-size: 12px;"><br></span></div></div></div><div>On googling that error I did find an old post where there was a temporary permissions issue:</div><div><a href="http://article.gmane.org/gmane.science.biology.ensembl.devel/8637/match=can+not+find+internal+name+species+metazoa">http://article.gmane.org/gmane.science.biology.ensembl.devel/8637/match=can+not+find+internal+name+species+metazoa</a></div><div><br></div><div>Is something like that happening again? (or, maybe I'm messing something up - it's been known!)</div><div><br></div><div>thanks very much,</div><div><br></div><div>Janet Young</div><div><br></div><div><div>------------------------------------------------------------------- </div><div><br></div><div>Dr. Janet Young </div><div><br></div><div>Malik lab</div><div><a href="http://research.fhcrc.org/malik/en.html">http://research.fhcrc.org/malik/en.html</a></div><div><br></div><div>Fred Hutchinson Cancer Research Center</div><div>1100 Fairview Avenue N., A2-025, </div><div>P.O. Box 19024, Seattle, WA 98109-1024, USA.</div><div><br></div><div>tel: (206) 667 4512</div><div>email: jayoung ...at... <a href="http://fhcrc.org">fhcrc.org</a></div><div><br></div><div>------------------------------------------------------------------- </div></div><div><br></div></body></html>