<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;" class="">Hi Francesco,<div class=""><br class=""></div><div class="">After discussing this issue with my colleagues.</div><div class=""><br class=""></div><div class="">Could you please test something?</div><div class=""><br class=""></div><div class="">In the file:</div><div class="">modules/Bio/EnsEMBL/Compara/GenomeDB.pm</div><div class=""><br class=""></div><div class="">Could you please comment lines 181, 182 and 184?</div><div class=""><br class=""></div><div class="">Just like this:</div><div class=""><br class=""></div><div class=""><div class=""></div></div><blockquote type="cite" class=""><div class=""><div class="">#assert_ref($dba, 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'db_adaptor');</div><div class="">#throw('$db_adaptor must refer to a Core database') unless $dba->group eq 'core';</div><div class="">$self->{'_db_adaptor'} = $dba;</div><div class="">#Bio::EnsEMBL::Compara::Utils::CoreDBAdaptor->pool_one_DBConnection($dba);</div></div></blockquote><div class=""><br class=""></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><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 23 Jan 2018, at 15:39, 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=""><div class=""><div class=""><div class=""><div class=""><div class="">Hi Mateus,<br class=""><br class=""></div>I have changed the order of some entries in the json file, it looks now like this:<br class=""><br class="">[<br class="">{<br class=""> "production_name" : "branchiostoma_floridae",<br class=""> "taxonomy_id" : "7739",<br class=""> "cds_fasta" : "/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/amphioxus_longest_CDS.fa",<br class=""> "prot_fasta" : "/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/amphioxus_longest_proteins.fa",<br class=""> "gene_coord_gff" : "/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/GCF_000003815.1_Version_2_genomic.gff",<br class=""> "source" : "refseq",<br class="">},<br class="">{<br class=""> "production_name" : "petromyzon_marinus",<br class=""> "taxonomy_id" : "7757",<br class=""> "cds_fasta" : "/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/sea_lamprey_CDS_no_monoexon.fa",<br class=""> "prot_fasta" : "/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/sea_lamprey_proteins_no_monoexon.fa",<br class=""> "gene_coord_gff" : "/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/PMZ_v3.1_genes.gtf",<br class=""> "source" : "augustus_maker",<br class="">},<br class="">]<br class=""><br class=""></div>but I get a different error message:<br class=""><br class="">Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] -> FETCH_INPUT<br class="">Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] -> RUN<br class="">ParamWarning: value for param('genome_component') is used before having been initialized!<br class="">ParamWarning: value for param('master_genome_db') is used before having been initialized!<br class="">Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] Fatal :<br class="">-------------------- EXCEPTION --------------------<br class="">MSG: db_adaptor's type 'Bio::EnsEMBL::Compara::GenomeMF' is not an ISA of 'Bio::EnsEMBL::DBSQL::DBAdaptor'<br class="">STACK Bio::EnsEMBL::Utils::Scalar::assert_ref_pp /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl/modules/Bio/EnsEMBL/Utils/Scalar.pm:231<br class="">STACK Bio::EnsEMBL::Compara::GenomeDB::db_adaptor /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm:181<br class="">STACK Bio::EnsEMBL::Compara::GenomeDB::new_from_DBAdaptor /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm:146<br class="">STACK Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB::create_genome_db /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/LoadOneGenomeDB.pm:204<br class="">STACK Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB::run /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/LoadOneGenomeDB.pm:186<br class="">STACK (eval) /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm:140<br class="">STACK Bio::EnsEMBL::Hive::Process::life_cycle /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm:127<br class="">STACK (eval) /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:688<br class="">STACK Bio::EnsEMBL::Hive::Worker::run_one_batch /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:674<br class="">STACK Bio::EnsEMBL::Hive::Worker::run /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:486<br class="">STACK (eval) /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Scripts/RunWorker.pm:88<br class="">STACK Bio::EnsEMBL::Hive::Scripts::RunWorker::runWorker /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Scripts/RunWorker.pm:94<br class="">STACK main::main /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/scripts/runWorker.pl:140<br class="">STACK toplevel /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/scripts/runWorker.pl:24<br class="">Date (localtime) = Tue Jan 23 16:29:39 2018<br class="">Ensembl API version = 91<br class="">---------------------------------------------------<br class=""><br class=""></div>Do you have any idea?<br class=""><br class=""></div>Cheers,<br class=""></div>Francesco<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2018-01-23 13:43 GMT+01:00 Mateus Patricio <span dir="ltr" class=""><<a href="mailto:mateus@ebi.ac.uk" target="_blank" class="">mateus@ebi.ac.uk</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi Francesco,<div class=""><br class=""></div><div class="">Could you please, check if your non_ensembl_species.json file is formatted like the one bellow:</div><div class=""><br class=""></div><div class=""><div class=""><font face="Courier New" class="">[</font></div><div class=""><font face="Courier New" class="">{</font></div><div class=""><font face="Courier New" class=""> "production_name" : "</font><span style="font-family:'Courier New'" class="">species_1</span><font face="Courier New" class="">",</font></div><div class=""><font face="Courier New" class=""> "taxonomy_id" : "1234",</font></div><div class=""><font face="Courier New" class=""> "cds_fasta" : "species_1.cds.fa",</font></div><div class=""><font face="Courier New" class=""> "prot_fasta" : "</font><span style="font-family:'Courier New'" class="">species_1</span><font face="Courier New" class="">.prot.fa",</font></div><div class=""><font face="Courier New" class=""> "gene_coord_gff" : "</font><span style="font-family:'Courier New'" class="">species_1</span><font face="Courier New" class="">.gff",</font></div><div class=""><font face="Courier New" class=""> "source" : "your_source",</font></div><div class=""><font face="Courier New" class="">},</font></div><div class=""><div class=""><font face="Courier New" class="">{</font></div><div class=""><font face="Courier New" class=""> "production_name" : "</font><span style="font-family:'Courier New'" class="">species_2</span><font face="Courier New" class="">",</font></div><div class=""><font face="Courier New" class=""> "taxonomy_id" : "4321",</font></div><div class=""><font face="Courier New" class=""> "cds_fasta" : "</font><span style="font-family:'Courier New'" class="">species_2</span><font face="Courier New" class="">.cds.fa",</font></div><div class=""><font face="Courier New" class=""> "prot_fasta" : "</font><span style="font-family:'Courier New'" class="">species_2</span><font face="Courier New" class="">.prot.fa",</font></div><div class=""><font face="Courier New" class=""> "gene_coord_gff" : "</font><span style="font-family:'Courier New'" class="">species_2</span><font face="Courier New" class="">.gff",</font></div><div class=""><font face="Courier New" class=""> "source" : "</font><span style="font-family:'Courier New'" class="">your_source</span><font face="Courier New" class="">",</font></div><div class=""><font face="Courier New" class="">},</font></div></div><div class=""><font face="Courier New" class="">]</font></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><div class=""><blockquote type="cite" class=""><div class=""><div class="h5"><div class="">On 23 Jan 2018, at 10:03, Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank" class="">francesco.lamanna@gmail.com</a>> wrote:</div><br class="m_-275209399951952603Apple-interchange-newline"></div></div><div class=""><div class=""><div class="h5"><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Hi all,<br class=""><br class=""></div>I am trying to build a members db using a set of core and custom genome assemblies. I have set up the locator column for both the core and custom databases in the genome_db table of the master database. However, when I run the LoadMembers pipeline, the load_genomedb analysis fails to load the custom genomes:<br class=""><br class="">mysql> SELECT * FROM msg;<br class="">+-------------+---------------<wbr class="">---------+----------------+---<wbr class="">-----+---------+-----------+--<wbr class="">-------------------+-------+--<wbr class="">------------+-----------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------+----------+<br class="">| analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> | is_error |<br class="">+-------------+---------------<wbr class="">---------+----------------+---<wbr class="">-----+---------+-----------+--<wbr class="">-------------------+-------+--<wbr class="">------------+-----------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------+----------+<br class="">| 3 | copy_table_from_master | 1 | 4 | 3 | 3 | 2018-01-22 18:00:51 | 0 | WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> | 0 |<br class="">| 3 | copy_table_from_master | 2 | 5 | 4 | 4 | 2018-01-22 18:03:12 | 0 | WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name' rows <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> <wbr class=""> | 0 |<br class="">| 5 | load_genomedb | 3 | 10 | 7 | 7 | 2018-01-22 18:05:17 | 0 | FETCH_INPUT | Sorry, could not figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::<wbr class="">GenomeMF/filename=/home/hd/hd_<wbr class="">hd/hd_cc141/Vertebrates_<wbr class="">project/Ensembl_compara/non_<wbr class="">ensembl_species.json;index=2' at /beegfs/home/hd/hd_hd/hd_<wbr class="">cc141/EnsEMBL/ensembl-hive/<wbr class="">modules/Bio/EnsEMBL/Hive/<wbr class="">Utils.pm line 366. | 1 |<br class="">| 5 | load_genomedb | 4 | 10 | 7 | 7 | 2018-01-22 18:05:18 | 1 | FETCH_INPUT | Sorry, could not figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::<wbr class="">GenomeMF/filename=/home/hd/hd_<wbr class="">hd/hd_cc141/Vertebrates_<wbr class="">project/Ensembl_compara/non_<wbr class="">ensembl_species.json;index=2' at /beegfs/home/hd/hd_hd/hd_<wbr class="">cc141/EnsEMBL/ensembl-hive/<wbr class="">modules/Bio/EnsEMBL/Hive/<wbr class="">Utils.pm line 366. | 1 |<br class="">| 5 | load_genomedb | 5 | 9 | 6 | 6 | 2018-01-22 18:05:19 | 0 | FETCH_INPUT | Sorry, could not figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::<wbr class="">GenomeMF/filename=/home/hd/hd_<wbr class="">hd/hd_cc141/Vertebrates_<wbr class="">project/Ensembl_compara/non_<wbr class="">ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_<wbr class="">cc141/EnsEMBL/ensembl-hive/<wbr class="">modules/Bio/EnsEMBL/Hive/<wbr class="">Utils.pm line 366. | 1 |<br class="">| 5 | load_genomedb | 6 | 9 | 6 | 6 | 2018-01-22 18:05:20 | 1 | FETCH_INPUT | Sorry, could not figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::<wbr class="">GenomeMF/filename=/home/hd/hd_<wbr class="">hd/hd_cc141/Vertebrates_<wbr class="">project/Ensembl_compara/non_<wbr class="">ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_<wbr class="">cc141/EnsEMBL/ensembl-hive/<wbr class="">modules/Bio/EnsEMBL/Hive/<wbr class="">Utils.pm line 366. | 1 |<br class="">| 5 | load_genomedb | 7 | 9 | 8 | 8 | 2018-01-22 18:06:08 | 2 | FETCH_INPUT | Sorry, could not figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::<wbr class="">GenomeMF/filename=/home/hd/hd_<wbr class="">hd/hd_cc141/Vertebrates_<wbr class="">project/Ensembl_compara/non_<wbr class="">ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_<wbr class="">cc141/EnsEMBL/ensembl-hive/<wbr class="">modules/Bio/EnsEMBL/Hive/<wbr class="">Utils.pm line 366. | 1 |<br class="">| 5 | load_genomedb | 8 | 10 | 8 | 8 | 2018-01-22 18:06:08 | 2 | FETCH_INPUT | Sorry, could not figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::<wbr class="">GenomeMF/filename=/home/hd/hd_<wbr class="">hd/hd_cc141/Vertebrates_<wbr class="">project/Ensembl_compara/non_<wbr class="">ensembl_species.json;index=2' at /beegfs/home/hd/hd_hd/hd_<wbr class="">cc141/EnsEMBL/ensembl-hive/<wbr class="">modules/Bio/EnsEMBL/Hive/<wbr class="">Utils.pm line 366. | 1 |<br class="">| 5 | load_genomedb | 9 | 9 | 10 | 10 | 2018-01-22 18:08:49 | 1 | FETCH_INPUT | Sorry, could not figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::<wbr class="">GenomeMF/filename=/home/hd/hd_<wbr class="">hd/hd_cc141/Vertebrates_<wbr class="">project/Ensembl_compara/non_<wbr class="">ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_<wbr class="">cc141/EnsEMBL/ensembl-hive/<wbr class="">modules/Bio/EnsEMBL/Hive/<wbr class="">Utils.pm line 366. | 1 |<br class="">+-------------+---------------<wbr class="">---------+----------------+---<wbr class="">-----+---------+-----------+--<wbr class="">-------------------+-------+--<wbr class="">------------+-----------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">------------------+----------+<br class="">9 rows in set (0.00 sec)<br class=""><br class=""></div>Any suggestion would be highly appreciated.<br class=""><br class=""></div>Cheers,<br class=""></div>Francesco<br class=""></div></div></div>
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