<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Francesco,<div class=""><br class=""></div><div class="">Could you please try adding the following to the locator field in the genome_db table for each of your custom genomes?</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class="">Bio::EnsEMBL::Compara::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.jsonindex=1</blockquote></div><div class=""><br class=""></div><div class="">Please match the index=1, index=2 to the order in which each genomes are declared in your file.</div><div class=""><br class=""></div><div class="">If your json file looks like this:</div><div class=""><br class=""></div><div class=""><font face="Courier New" class="">{</font></div><div class=""><font face="Courier New" class=""> "production_name" : "species1",</font></div><div class=""><font face="Courier New" class=""> "taxonomy_id" : "8508",</font></div><div class=""><font face="Courier New" class=""> "cds_fasta" : “species1.cds.fa",</font></div><div class=""><font face="Courier New" class=""> "prot_fasta" : "species1.prot.fa",</font></div><div class=""><font face="Courier New" class=""> "gene_coord_gff" : "species1.gff",</font></div><div class=""><font face="Courier New" class=""> "source" : "augustus_maker",</font></div><div class=""><font face="Courier New" class="">},</font></div><div class=""><font face="Courier New" class=""><br class=""></font></div><div class=""><font face="Courier New" class="">{</font></div><div class=""><font face="Courier New" class=""> "production_name" : "species2",</font></div><div class=""><font face="Courier New" class=""> "taxonomy_id" : "8496",</font></div><div class=""><font face="Courier New" class=""> "cds_fasta" : “species2.cds.fa",</font></div><div class=""><font face="Courier New" class=""> "prot_fasta" : “species2.prot.fa",</font></div><div class=""><font face="Courier New" class=""> "gene_coord_gff" : "species2.gff",</font></div><div class=""><font face="Courier New" class=""> "source" : "refseq",</font></div><div class=""><span style="font-family: 'Courier New';" class="">},</span> </div><div class=""><br class=""></div><div class="">You could add this info to the genome_db table:</div><div class=""><br class=""></div><div class=""><font face="Courier New" class="">INSERT INTO genome_db (locator) VALUES ('Bio::EnsEMBL::Compara::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.jsonindex=1’) WHERE name = ’species1'</font></div><div class=""><font face="Courier New" class="">INSERT INTO genome_db (locator) VALUES ('Bio::EnsEMBL::Compara::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.jsonindex=2’) WHERE name = ’species2’</font></div><div class=""><font face="Courier New" class=""><br class=""></font></div><div class="">I hope that helps.</div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Mateus.</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 14 Dec 2017, at 17:17, Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" class="">francesco.lamanna@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi all,<br class=""><div class=""><br class="">I am trying to run the Compara
protein-tree pipeline (v91) on a set of two core ensembl genomes and
three custom genomes (stored locally) using a master database.</div><div class=""><br class=""></div><div class="">when I run <a href="http://beekeeper.pl/" class="">beekeeper.pl</a> script load_genomedb fails to find my local genomes (but it loads correctly the ensembl core genomes), and drops this kind of error message:</div><div class=""><br class=""></div><div class="">Could not
find species_name='petromyzon_marin<wbr class="">us', assembly_name='germline_final' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMB<wbr class="">L/ensembl-compara/modules/Bio/<wbr class="">EnsEMBL/Compara/RunnableDB/<wbr class="">LoadOneGenomeDB.pm line 179.</div><div class=""><br class=""></div><div class="">the information regarding the local genomes is stored in a .json file and loaded in the genome_db table of the master database. The .json file is invoked in pipeline conf script using:</div><div class=""><br class=""></div><div class="">'curr_file_sources_locs' => [ '/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.json' ]</div><div class=""><br class=""></div><div class="">Thank you for your help,</div><div class="">Francesco.<br class=""></div><div class=""><span class="gmail-gI"><span class=""></span></span></div></div>
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