[ensembl-dev] Problem with locator in LoadMembers.pm (ensembl-compara)
Mateus Patricio
mateus at ebi.ac.uk
Thu Jan 25 14:39:40 GMT 2018
Hi Francesco,
After discussing this issue with my colleagues.
Could you please test something?
In the file:
modules/Bio/EnsEMBL/Compara/GenomeDB.pm
Could you please comment lines 181, 182 and 184?
Just like this:
> #assert_ref($dba, 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'db_adaptor');
> #throw('$db_adaptor must refer to a Core database') unless $dba->group eq 'core';
> $self->{'_db_adaptor'} = $dba;
> #Bio::EnsEMBL::Compara::Utils::CoreDBAdaptor->pool_one_DBConnection($dba);
I hope that helps.
Cheers,
Mateus.
> On 23 Jan 2018, at 15:39, Francesco Lamanna <francesco.lamanna at gmail.com> wrote:
>
> Hi Mateus,
>
> I have changed the order of some entries in the json file, it looks now like this:
>
> [
> {
> "production_name" : "branchiostoma_floridae",
> "taxonomy_id" : "7739",
> "cds_fasta" : "/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/amphioxus_longest_CDS.fa",
> "prot_fasta" : "/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/amphioxus_longest_proteins.fa",
> "gene_coord_gff" : "/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/GCF_000003815.1_Version_2_genomic.gff",
> "source" : "refseq",
> },
> {
> "production_name" : "petromyzon_marinus",
> "taxonomy_id" : "7757",
> "cds_fasta" : "/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/sea_lamprey_CDS_no_monoexon.fa",
> "prot_fasta" : "/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/sea_lamprey_proteins_no_monoexon.fa",
> "gene_coord_gff" : "/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/PMZ_v3.1_genes.gtf",
> "source" : "augustus_maker",
> },
> ]
>
> but I get a different error message:
>
> Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] -> FETCH_INPUT
> Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] -> RUN
> ParamWarning: value for param('genome_component') is used before having been initialized!
> ParamWarning: value for param('master_genome_db') is used before having been initialized!
> Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] Fatal :
> -------------------- EXCEPTION --------------------
> MSG: db_adaptor's type 'Bio::EnsEMBL::Compara::GenomeMF' is not an ISA of 'Bio::EnsEMBL::DBSQL::DBAdaptor'
> STACK Bio::EnsEMBL::Utils::Scalar::assert_ref_pp /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl/modules/Bio/EnsEMBL/Utils/Scalar.pm:231
> STACK Bio::EnsEMBL::Compara::GenomeDB::db_adaptor /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm:181
> STACK Bio::EnsEMBL::Compara::GenomeDB::new_from_DBAdaptor /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm:146
> 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
> STACK Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB::run /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/LoadOneGenomeDB.pm:186
> STACK (eval) /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm:140
> STACK Bio::EnsEMBL::Hive::Process::life_cycle /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm:127
> STACK (eval) /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:688
> 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
> STACK Bio::EnsEMBL::Hive::Worker::run /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:486
> STACK (eval) /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Scripts/RunWorker.pm:88
> 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
> STACK main::main /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/scripts/runWorker.pl:140
> STACK toplevel /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/scripts/runWorker.pl:24
> Date (localtime) = Tue Jan 23 16:29:39 2018
> Ensembl API version = 91
> ---------------------------------------------------
>
> Do you have any idea?
>
> Cheers,
> Francesco
>
> 2018-01-23 13:43 GMT+01:00 Mateus Patricio <mateus at ebi.ac.uk <mailto:mateus at ebi.ac.uk>>:
> Hi Francesco,
>
> Could you please, check if your non_ensembl_species.json file is formatted like the one bellow:
>
> [
> {
> "production_name" : "species_1",
> "taxonomy_id" : "1234",
> "cds_fasta" : "species_1.cds.fa",
> "prot_fasta" : "species_1.prot.fa",
> "gene_coord_gff" : "species_1.gff",
> "source" : "your_source",
> },
> {
> "production_name" : "species_2",
> "taxonomy_id" : "4321",
> "cds_fasta" : "species_2.cds.fa",
> "prot_fasta" : "species_2.prot.fa",
> "gene_coord_gff" : "species_2.gff",
> "source" : "your_source",
> },
> ]
>
> Cheers,
>
> Mateus.
>
>
>> On 23 Jan 2018, at 10:03, Francesco Lamanna <francesco.lamanna at gmail.com <mailto:francesco.lamanna at gmail.com>> wrote:
>>
>> Hi all,
>>
>> 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:
>>
>> mysql> SELECT * FROM msg;
>> +-------------+------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
>> | analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg | is_error |
>> +-------------+------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
>> | 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 |
>> | 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 |
>> | 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 |
>> | 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 |
>> | 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 |
>> | 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 |
>> | 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 |
>> | 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 |
>> | 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 |
>> +-------------+------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
>> 9 rows in set (0.00 sec)
>>
>> Any suggestion would be highly appreciated.
>>
>> Cheers,
>> Francesco
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>
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