<div dir="ltr"><div><div><div><div><div>Hi Mateus,<br><br></div>I have changed the order of some entries in the json file, it looks now like this:<br><br>[<br>{<br> "production_name" : "branchiostoma_floridae",<br> "taxonomy_id" : "7739",<br> "cds_fasta" : "/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/amphioxus_longest_CDS.fa",<br> "prot_fasta" : "/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/amphioxus_longest_proteins.fa",<br> "gene_coord_gff" : "/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/GCF_000003815.1_Version_2_genomic.gff",<br> "source" : "refseq",<br>},<br>{<br> "production_name" : "petromyzon_marinus",<br> "taxonomy_id" : "7757",<br> "cds_fasta" : "/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/sea_lamprey_CDS_no_monoexon.fa",<br> "prot_fasta" : "/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/sea_lamprey_proteins_no_monoexon.fa",<br> "gene_coord_gff" : "/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/PMZ_v3.1_genes.gtf",<br> "source" : "augustus_maker",<br>},<br>]<br><br></div>but I get a different error message:<br><br>Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] -> FETCH_INPUT<br>Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] -> RUN<br>ParamWarning: value for param('genome_component') is used before having been initialized!<br>ParamWarning: value for param('master_genome_db') is used before having been initialized!<br>Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] Fatal :<br>-------------------- EXCEPTION --------------------<br>MSG: db_adaptor's type 'Bio::EnsEMBL::Compara::GenomeMF' is not an ISA of 'Bio::EnsEMBL::DBSQL::DBAdaptor'<br>STACK Bio::EnsEMBL::Utils::Scalar::assert_ref_pp /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl/modules/Bio/EnsEMBL/Utils/Scalar.pm:231<br>STACK Bio::EnsEMBL::Compara::GenomeDB::db_adaptor /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm:181<br>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>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>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>STACK (eval) /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm:140<br>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>STACK (eval) /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:688<br>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>STACK Bio::EnsEMBL::Hive::Worker::run /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:486<br>STACK (eval) /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Scripts/RunWorker.pm:88<br>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>STACK main::main /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/scripts/runWorker.pl:140<br>STACK toplevel /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/scripts/runWorker.pl:24<br>Date (localtime) = Tue Jan 23 16:29:39 2018<br>Ensembl API version = 91<br>---------------------------------------------------<br><br></div>Do you have any idea?<br><br></div>Cheers,<br></div>Francesco<br></div><div class="gmail_extra"><br><div class="gmail_quote">2018-01-23 13:43 GMT+01:00 Mateus Patricio <span dir="ltr"><<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Francesco,<div><br></div><div>Could you please, check if your non_ensembl_species.json file is formatted like the one bellow:</div><div><br></div><div><div><font face="Courier New">[</font></div><div><font face="Courier New">{</font></div><div><font face="Courier New"> "production_name" : "</font><span style="font-family:'Courier New'">species_1</span><font face="Courier New">",</font></div><div><font face="Courier New"> "taxonomy_id" : "1234",</font></div><div><font face="Courier New"> "cds_fasta" : "species_1.cds.fa",</font></div><div><font face="Courier New"> "prot_fasta" : "</font><span style="font-family:'Courier New'">species_1</span><font face="Courier New">.prot.fa",</font></div><div><font face="Courier New"> "gene_coord_gff" : "</font><span style="font-family:'Courier New'">species_1</span><font face="Courier New">.gff",</font></div><div><font face="Courier New"> "source" : "your_source",</font></div><div><font face="Courier New">},</font></div><div><div><font face="Courier New">{</font></div><div><font face="Courier New"> "production_name" : "</font><span style="font-family:'Courier New'">species_2</span><font face="Courier New">",</font></div><div><font face="Courier New"> "taxonomy_id" : "4321",</font></div><div><font face="Courier New"> "cds_fasta" : "</font><span style="font-family:'Courier New'">species_2</span><font face="Courier New">.cds.fa",</font></div><div><font face="Courier New"> "prot_fasta" : "</font><span style="font-family:'Courier New'">species_2</span><font face="Courier New">.prot.fa",</font></div><div><font face="Courier New"> "gene_coord_gff" : "</font><span style="font-family:'Courier New'">species_2</span><font face="Courier New">.gff",</font></div><div><font face="Courier New"> "source" : "</font><span style="font-family:'Courier New'">your_source</span><font face="Courier New">",</font></div><div><font face="Courier New">},</font></div></div><div><font face="Courier New">]</font></div><div><br></div><div>Cheers,</div><div><br></div><div>Mateus.</div><div><br></div><div><br></div><div><blockquote type="cite"><div><div class="h5"><div>On 23 Jan 2018, at 10:03, Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a>> wrote:</div><br class="m_-275209399951952603Apple-interchange-newline"></div></div><div><div><div class="h5"><div dir="ltr"><div><div><div><div>Hi all,<br><br></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><br>mysql> SELECT * FROM msg;<br>+-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------+----------+<br>| analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg <wbr> <wbr> <wbr> <wbr> <wbr> <wbr> <wbr> <wbr> <wbr> <wbr> | is_error |<br>+-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------+----------+<br>| 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> <wbr> <wbr> <wbr> <wbr> <wbr> <wbr> <wbr> | 0 |<br>| 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> <wbr> <wbr> <wbr> <wbr> <wbr> <wbr> <wbr> | 0 |<br>| 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>GenomeMF/filename=/home/hd/hd_<wbr>hd/hd_cc141/Vertebrates_<wbr>project/Ensembl_compara/non_<wbr>ensembl_species.json;index=2' at /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Utils.pm line 366. | 1 |<br>| 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>GenomeMF/filename=/home/hd/hd_<wbr>hd/hd_cc141/Vertebrates_<wbr>project/Ensembl_compara/non_<wbr>ensembl_species.json;index=2' at /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Utils.pm line 366. | 1 |<br>| 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>GenomeMF/filename=/home/hd/hd_<wbr>hd/hd_cc141/Vertebrates_<wbr>project/Ensembl_compara/non_<wbr>ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Utils.pm line 366. | 1 |<br>| 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>GenomeMF/filename=/home/hd/hd_<wbr>hd/hd_cc141/Vertebrates_<wbr>project/Ensembl_compara/non_<wbr>ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Utils.pm line 366. | 1 |<br>| 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>GenomeMF/filename=/home/hd/hd_<wbr>hd/hd_cc141/Vertebrates_<wbr>project/Ensembl_compara/non_<wbr>ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Utils.pm line 366. | 1 |<br>| 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>GenomeMF/filename=/home/hd/hd_<wbr>hd/hd_cc141/Vertebrates_<wbr>project/Ensembl_compara/non_<wbr>ensembl_species.json;index=2' at /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Utils.pm line 366. | 1 |<br>| 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>GenomeMF/filename=/home/hd/hd_<wbr>hd/hd_cc141/Vertebrates_<wbr>project/Ensembl_compara/non_<wbr>ensembl_species.json;index=1' at /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Utils.pm line 366. | 1 |<br>+-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------+----------+<br>9 rows in set (0.00 sec)<br><br></div>Any suggestion would be highly appreciated.<br><br></div>Cheers,<br></div>Francesco<br></div></div></div>
______________________________<wbr>_________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/<wbr>mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br></div></blockquote></div><br></div></div><br>______________________________<wbr>_________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/<wbr>mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>