<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; "><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;">Hi,</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>We have a custom Compara database for our 50 helminth genomes project, built by a bioinformatician in our team.</div><div><br></div><div>I have been trying to get all homologies for a gene tree using the root_id of the tree, like so:</div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><br></blockquote><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><div><font face="Andale Mono">my $root_node_id = $gene_tree->root_id();<span class="Apple-tab-span" style="white-space: pre; "> </span></font></div></div><div><font face="Andale Mono">my $homologies = $homology_adaptor->fetch_all_by_tree_node_id($root_node_id);</font></div></blockquote><div><br></div><div>This throws the following error:</div><div><br></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><font face="Andale Mono">-------------------- EXCEPTION --------------------</font></div><div><font face="Andale Mono">MSG: Detected an error whilst executing SQL 'SELECT h.homology_id, h.method_link_species_set_id, h.description, <a href="http://h.is/">h.is</a>_tree_compliant, h.dn, h.ds, h.n, h.s, h.lnl, h.species_tree_node_id, h.gene_tree_node_id, h.gene_tree_root_id FROM (homology h) WHERE h.tree_node_id = ? ': DBD::mysql::st execute failed: Unknown column 'h.tree_node_id' in 'where clause' at /nfs/users/nfs_b/bh4/apps/ensembl-74/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm line 168.</font></div><div><font face="Andale Mono"><br></font></div><div><font face="Andale Mono">STACK Bio::EnsEMBL::Compara::DBSQL::BaseAdaptor::generic_fetch /nfs/users/nfs_b/bh4/apps/ensembl-74/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm:170</font></div><div><font face="Andale Mono">STACK Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor::fetch_all_by_tree_node_id /nfs/users/nfs_b/bh4/apps/ensembl-74/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/HomologyAdaptor.pm:255</font></div><div><font face="Andale Mono">STACK (eval) (eval 82)[/usr/share/perl/5.14/perl5db.pl:640]:2</font></div><div><font face="Andale Mono">STACK DB::eval /usr/share/perl/5.14/perl5db.pl:640</font></div><div><font face="Andale Mono">STACK DB::DB /usr/share/perl/5.14/perl5db.pl:3436</font></div><div><font face="Andale Mono">STACK main::get_all_one_to_one_orthologs /nfs/users/nfs_b/bh4/git/helminth_scripts/scripts/get_fasta_for_one2one_orthologs_from_gene_trees_v74.pl:75</font></div><div><font face="Andale Mono">STACK toplevel /nfs/users/nfs_b/bh4/git/helminth_scripts/scripts/get_fasta_for_one2one_orthologs_from_gene_trees_v74.pl:43</font></div><div><font face="Andale Mono">Date (localtime) = Tue Feb 18 13:47:22 2014</font></div><div><font face="Andale Mono">Ensembl API version = 74</font></div><div><font face="Andale Mono">---------------------------------------------------</font></div></blockquote><div><br></div><div>I can confirm that both our database and the API I'm using are version 74.</div><div><br></div><div>The offending line is line 252 in Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor.</div><div>Turns out that there is no '<b>tree_node_id</b>' field in the homology table in the new release. Should this be '<b>h.gene_tree_node_id = ?</b>' instead?</div><div><br></div><div>Regards,</div><div>Bhavana</div><div><br></div><div><br></div><div>
<div style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><br class="Apple-interchange-newline">---------------------------------------------</div><div>Bhavana Harsha</div><div>Bioinformatician</div><div>Parasite Genomics</div><div>Wellcome Trust Sanger Institute</div><div>Hinxton, UK</div><div>CB10 1SA</div></div><div><br></div></div><br class="Apple-interchange-newline" style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><br class="Apple-interchange-newline">
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