[ensembl-dev] Problem with genome_member_copy (Compara).
Mateus Patricio
mateus at ebi.ac.uk
Thu Jan 11 11:01:26 GMT 2018
Hi Francesco,
In your case the solution should be starting the LoadMembers without the option “--collection ensembl”.
If you start the pipeline without it, it should use all the current species in your master database.
In Ensembl we have different collections that are used for different purposes, and the default one is “ensembl”.
Please let me know if this works.
Cheers,
Mateus.
> On 11 Jan 2018, at 10:13, Francesco Lamanna <francesco.lamanna at gmail.com> wrote:
>
> Hi Mateus,
>
> many thanks for your answer.
>
> I am trying to launch the LoadMembers pipeline in order to make a member_db, but I get the following error:
>
> 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 | 2018-01-11 11:04:02 | 0 | WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows | 0 |
> | 3 | copy_table_from_master | 2 | 5 | 4 | 4 | 2018-01-11 11:05:46 | 0 | WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name' rows | 0 |
> | 4 | load_genomedb_factory | 3 | 3 | 5 | 5 | 2018-01-11 11:07:06 | 0 | FETCH_INPUT | Could not fetch collection ss with name=ensembl at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/GenomeDBFactory.pm line 106. | 1 |
> | 4 | load_genomedb_factory | 4 | 3 | 6 | 6 | 2018-01-11 11:08:00 | 1 | FETCH_INPUT | Could not fetch collection ss with name=ensembl at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/GenomeDBFactory.pm line 106. | 1 |
> | 4 | load_genomedb_factory | 5 | 3 | 7 | 7 | 2018-01-11 11:08:25 | 2 | FETCH_INPUT | Could not fetch collection ss with name=ensembl at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/GenomeDBFactory.pm line 106. | 1 |
> | 4 | load_genomedb_factory | 6 | 3 | 8 | 8 | 2018-01-11 11:09:25 | 3 | FETCH_INPUT | Could not fetch collection ss with name=ensembl at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/GenomeDBFactory.pm line 106. | 1 |
> +-------------+------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
> 6
>
> Cheers,
> Francesco.
>
> 2018-01-10 17:31 GMT+01:00 Mateus Patricio <mateus at ebi.ac.uk <mailto:mateus at ebi.ac.uk>>:
> 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 <http://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 <mailto: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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>
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