[ensembl-dev] Problem with locator in LoadMembers.pm (ensembl-compara)

[Francesco Lamanna]

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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