<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="">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><blockquote type="cite" class=""><div class="">On 23 Jan 2018, at 10:03, 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="">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="">+-------------+------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br class="">| analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg | is_error |<br 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 | 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 | 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::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.json;index=2' at /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/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::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.json;index=2' at /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/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::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/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::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/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::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/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::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.json;index=2' at /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/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::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Utils.pm line 366. | 1 |<br 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>
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