<div dir="ltr"><div><div><div><div>Hi Mateus,<br><br></div>I am using release/91 of GenomeDB.pm (it misses Bio::EnsEMBL::Compara::Utils:<wbr>:CoreDBAdaptor->pool_one_<wbr>DBConnection($dba); at line 184).<br><br></div>Anyway, if I comment lines 181 and 182 I get the following error:<br><br>mysql> SELECT * FROM msg;<br>+-------------+------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br>| analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg | is_error |<br>+-------------+------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br>| 3 | copy_table_from_master | 1 | 4 | 3 | 3 | 2018-01-25 17:19:47 | 0 | WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows | 0 |<br>| 3 | copy_table_from_master | 2 | 5 | 4 | 4 | 2018-01-25 17:23:03 | 0 | WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name' rows | 0 |<br>| 5 | load_genomedb | 3 | 9 | 7 | 7 | 2018-01-25 17:24:19 | 0 | RUN | Can't call method "connected" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 186. | 1 |<br>| 5 | load_genomedb | 4 | 10 | 7 | 7 | 2018-01-25 17:24:21 | 0 | RUN | Can't call method "connected" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 186. | 1 |<br>| 5 | load_genomedb | 5 | 9 | 6 | 6 | 2018-01-25 17:24:26 | 1 | RUN | Can't call method "connected" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 186. | 1 |<br>| 5 | load_genomedb | 6 | 10 | 6 | 6 | 2018-01-25 17:24:27 | 1 | RUN | Can't call method "connected" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 186. | 1 |<br>| 5 | load_genomedb | 7 | 9 | 8 | 8 | 2018-01-25 17:25:19 | 2 | RUN | Can't call method "connected" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 186. | 1 |<br>| 5 | load_genomedb | 8 | 10 | 8 | 8 | 2018-01-25 17:25:20 | 2 | RUN | Can't call method "connected" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 186. | 1 |<br>+-------------+------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br><br></div>It looks like GenomeDB is now missing something.</div><div><br></div><div>Additionally, if I run the analysis in debug mode, I get these two warnings:</div><div><br></div><div>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 10 ] Fatal : Can't call method "connected" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 186.<br></div><div><br></div><div>Thanks,</div><div>Francesco.<br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2018-01-25 15:39 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>After discussing this issue with my colleagues.</div><div><br></div><div>Could you please test something?</div><div><br></div><div>In the file:</div><div>modules/Bio/EnsEMBL/Compara/<wbr>GenomeDB.pm</div><div><br></div><div>Could you please comment lines 181, 182 and 184?</div><div><br></div><div>Just like this:</div><div><br></div><div><div></div></div><blockquote type="cite"><div><div>#assert_ref($dba, 'Bio::EnsEMBL::DBSQL::<wbr>DBAdaptor', 'db_adaptor');</div><div>#throw('$db_adaptor must refer to a Core database') unless $dba->group eq 'core';</div><div>$self->{'_db_adaptor'} = $dba;</div><div>#Bio::EnsEMBL::Compara::Utils:<wbr>:CoreDBAdaptor->pool_one_<wbr>DBConnection($dba);</div></div></blockquote><div><br></div><div>I hope that helps.</div><div><br></div><div>Cheers,</div><div><br></div><div>Mateus.</div><div><div class="h5"><div><br></div><div><br></div><div><br><div><blockquote type="cite"><div>On 23 Jan 2018, at 15:39, Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a>> wrote:</div><br class="m_-2371849104535116781Apple-interchange-newline"><div><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/<wbr>Genomes/amphioxus/NCBI/<wbr>amphioxus_longest_CDS.fa",<br> "prot_fasta" : "/home/hd/hd_hd/hd_cc141/<wbr>Genomes/amphioxus/NCBI/<wbr>amphioxus_longest_proteins.fa"<wbr>,<br> "gene_coord_gff" : "/home/hd/hd_hd/hd_cc141/<wbr>Genomes/amphioxus/NCBI/GCF_<wbr>000003815.1_Version_2_genomic.<wbr>gff",<br> "source" : "refseq",<br>},<br>{<br> "production_name" : "petromyzon_marinus",<br> "taxonomy_id" : "7757",<br> "cds_fasta" : "/home/hd/hd_hd/hd_cc141/<wbr>Lamprey_annotation/germ_final/<wbr>PMZ_v3.1_final/sea_lamprey_<wbr>CDS_no_monoexon.fa",<br> "prot_fasta" : "/home/hd/hd_hd/hd_cc141/<wbr>Lamprey_annotation/germ_final/<wbr>PMZ_v3.1_final/sea_lamprey_<wbr>proteins_no_monoexon.fa",<br> "gene_coord_gff" : "/home/hd/hd_hd/hd_cc141/<wbr>Lamprey_annotation/germ_final/<wbr>PMZ_v3.1_final/PMZ_v3.1_genes.<wbr>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::<wbr>GenomeMF' is not an ISA of 'Bio::EnsEMBL::DBSQL::<wbr>DBAdaptor'<br>STACK Bio::EnsEMBL::Utils::Scalar::<wbr>assert_ref_pp /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl/modules/Bio/<wbr>EnsEMBL/Utils/Scalar.pm:231<br>STACK Bio::EnsEMBL::Compara::<wbr>GenomeDB::db_adaptor /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>GenomeDB.pm:181<br>STACK Bio::EnsEMBL::Compara::<wbr>GenomeDB::new_from_DBAdaptor /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>GenomeDB.pm:146<br>STACK Bio::EnsEMBL::Compara::<wbr>RunnableDB::LoadOneGenomeDB::<wbr>create_genome_db /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm:<wbr>204<br>STACK Bio::EnsEMBL::Compara::<wbr>RunnableDB::LoadOneGenomeDB::<wbr>run /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm:<wbr>186<br>STACK (eval) /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Process.pm:140<br>STACK Bio::EnsEMBL::Hive::Process::<wbr>life_cycle /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Process.pm:127<br>STACK (eval) /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Worker.pm:688<br>STACK Bio::EnsEMBL::Hive::Worker::<wbr>run_one_batch /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Worker.pm:674<br>STACK Bio::EnsEMBL::Hive::Worker::<wbr>run /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Worker.pm:486<br>STACK (eval) /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Scripts/RunWorker.pm:88<br>STACK Bio::EnsEMBL::Hive::Scripts::<wbr>RunWorker::runWorker /beegfs/home/hd/hd_hd/hd_<wbr>cc141/EnsEMBL/ensembl-hive/<wbr>modules/Bio/EnsEMBL/Hive/<wbr>Scripts/RunWorker.pm:94<br>STACK main::main /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-hive/scripts/<wbr>runWorker.pl:140<br>STACK toplevel /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-hive/scripts/<wbr>runWorker.pl:24<br>Date (localtime) = Tue Jan 23 16:29:39 2018<br>Ensembl API version = 91<br>------------------------------<wbr>---------------------<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="m_-2371849104535116781h5"><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_-2371849104535116781m_-275209399951952603Apple-interchange-newline"></div></div><div><div><div class="m_-2371849104535116781h5"><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::Genome<wbr>MF/filename=/home/hd/hd_hd/hd_<wbr>cc141/Vertebrates_project/<wbr>Ensembl_compara/non_ensembl_<wbr>species.json;index=2' at /beegfs/home/hd/hd_hd/hd_cc141<wbr>/EnsEMBL/ensembl-hive/modules/<wbr>Bio/EnsEMBL/Hive/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::Genome<wbr>MF/filename=/home/hd/hd_hd/hd_<wbr>cc141/Vertebrates_project/<wbr>Ensembl_compara/non_ensembl_<wbr>species.json;index=2' at /beegfs/home/hd/hd_hd/hd_cc141<wbr>/EnsEMBL/ensembl-hive/modules/<wbr>Bio/EnsEMBL/Hive/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::Genome<wbr>MF/filename=/home/hd/hd_hd/hd_<wbr>cc141/Vertebrates_project/<wbr>Ensembl_compara/non_ensembl_<wbr>species.json;index=1' at /beegfs/home/hd/hd_hd/hd_cc141<wbr>/EnsEMBL/ensembl-hive/modules/<wbr>Bio/EnsEMBL/Hive/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::Genome<wbr>MF/filename=/home/hd/hd_hd/hd_<wbr>cc141/Vertebrates_project/<wbr>Ensembl_compara/non_ensembl_<wbr>species.json;index=1' at /beegfs/home/hd/hd_hd/hd_cc141<wbr>/EnsEMBL/ensembl-hive/modules/<wbr>Bio/EnsEMBL/Hive/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::Genome<wbr>MF/filename=/home/hd/hd_hd/hd_<wbr>cc141/Vertebrates_project/<wbr>Ensembl_compara/non_ensembl_<wbr>species.json;index=1' at /beegfs/home/hd/hd_hd/hd_cc141<wbr>/EnsEMBL/ensembl-hive/modules/<wbr>Bio/EnsEMBL/Hive/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::Genome<wbr>MF/filename=/home/hd/hd_hd/hd_<wbr>cc141/Vertebrates_project/<wbr>Ensembl_compara/non_ensembl_<wbr>species.json;index=2' at /beegfs/home/hd/hd_hd/hd_cc141<wbr>/EnsEMBL/ensembl-hive/modules/<wbr>Bio/EnsEMBL/Hive/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::Genome<wbr>MF/filename=/home/hd/hd_hd/hd_<wbr>cc141/Vertebrates_project/<wbr>Ensembl_compara/non_ensembl_<wbr>species.json;index=1' at /beegfs/home/hd/hd_hd/hd_cc141<wbr>/EnsEMBL/ensembl-hive/modules/<wbr>Bio/EnsEMBL/Hive/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>
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