[ensembl-dev] Problem with locator in LoadMembers.pm (ensembl-compara)
Mateus Patricio
mateus at ebi.ac.uk
Tue Jan 23 12:43:06 GMT 2018
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> 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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