[ensembl-dev] Problem with genome_member_copy (Compara).

[Mateus Patricio]

Hi Francesco

The protein tree pipeline reuses the genes and sequence members from the 'reuse_db' parameter, which in this case should point to a members database.

This members database can be created by running the LoadMembers pipeline.

You can initiate the pipeline with the following command line:

init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::EBI::Ensembl::LoadMembers_conf --collection ensembl

Then you should point the parameter reuse_db to this database on your Protein Tree config file.

'reuse_db'   => 'mysql://ensro@host:port/database',

Please do let me know if you have further questions.

Cheers,

Mateus.


> On 10 Jan 2018, at 16:06, Francesco Lamanna <francesco.lamanna at gmail.com> wrote:
> 
> Hi all,
> 
> when I try to run the protein tree pipeline (v91) using the core Human and Chicken genomes I get the following error message:
> 
> mysql> SELECT * from msg;
> +-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------------------------------+----------+
> | analysis_id | logic_name                    | log_message_id | job_id | role_id | worker_id | when_logged         | retry | status       | msg                                                                                | is_error |
> +-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------------------------------+----------+
> |           9 | copy_ncbi_table               |              1 |      5 |       3 |         4 | 2018-01-10 16:40:13 |     0 | WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows                                  |        0 |
> |           9 | copy_ncbi_table               |              2 |      6 |       4 |         3 | 2018-01-10 16:42:04 |     0 | WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name' rows                                  |        0 |
> |          10 | populate_method_links_from_db |              3 |      7 |       6 |         6 | 2018-01-10 16:43:44 |     0 | WRITE_OUTPUT | Successfully copied 18 'method_link' rows                                          |        0 |
> |          25 | genome_member_copy            |              4 |     13 |      11 |        11 | 2018-01-10 16:47:49 |     0 | FETCH_INPUT  | ParamError: value for param_required('reuse_db') is required and has to be defined |        1 |
> |          25 | genome_member_copy            |              5 |     14 |      12 |        12 | 2018-01-10 16:47:49 |     0 | FETCH_INPUT  | ParamError: value for param_required('reuse_db') is required and has to be defined |        1 |
> +-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------------------------------+----------+
> 
> I have no clue about what to put in the 'reuse_db' parameter (nor could I find any information in the compara docs). 
> 
> Can anyone please help me to solve this issue?
> 
> Thanks,
> Francesco.
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