<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>Hello,</div><div> I am having a problem creating the adaptor to the Ensembl compara’s homology database.</div><div><b>My code:</b></div><div><div>my $homology_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi', 'compara', 'Homology'); die "homology adaptor fail\n" if !defined $homology_adaptor;</div></div><div><b><br></b></div><div><b>My output:</b></div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><b>----------</b>---------- WARNING ----------------------</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">MSG: 'Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor' cannot be found.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Exception Can't locate feature.pm in @INC (@INC contains: /usr/local/src/ensembl-75/ensembl-funcgen/modules /usr/local/src/ensembl-75/ensembl-variation/modules /usr/local/src/ensembl-75/ensembl-compara/modules /usr/local/src/ensembl-75/ensembl/modules /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMember.pm line 75.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">BEGIN failed--compilation aborted at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMember.pm line 75.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Compilation failed in require at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMemberSet.pm line 86.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">BEGIN failed--compilation aborted at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/AlignedMemberSet.pm line 86.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Compilation failed in require at (eval 234) line 3.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"> </span>...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">BEGIN failed--compilation aborted at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/Homology.pm line 76.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Compilation failed in require at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm line 24.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">BEGIN failed--compilation aborted at /usr/local/src/ensembl-75/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm line 24.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Compilation failed in require at (eval 233) line 3.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo; min-height: 13px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo; min-height: 13px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">FILE: Bio/EnsEMBL/Registry.pm LINE: 1040</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">CALLED BY: get_paralogs.pl LINE: 45</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Date (localtime) = Wed Mar 19 16:38:34 2014</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Ensembl API version = 75</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">---------------------------------------------------</div></div><div><br></div><div><b>Additional notes:</b></div><div>1) I have already checked that the compara is installed and in my script, I already linked to the modules using:</div><div>use lib '/usr/local/src/ensembl-75/ensembl-compara/modules’;</div><div>use Bio::EnsEMBL::Registry;</div><div><br></div><div>2) The following code works:</div><div><div>my $gene_member_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi', 'compara', 'GeneMember'); die "gene member adaptor fail\n" if !defined $gene_member_adaptor;</div></div><div>It seems that I can connect to GeneMember for compara no problem, but fails when I replace “GeneMember" with “Homology"</div><div><br></div><div>Any suggestion is greatly appreciated! Thanks!</div><div apple-content-edited="true">
<div>Casper Shyr</div><div>PhD Candidate, Centre for Molecular Medicine and Therapeutics</div><div>University of British Columbia</div><div><a href="mailto:casper@cmmt.ubc.ca">casper@cmmt.ubc.ca</a></div><div><br></div><br class="Apple-interchange-newline">
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