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

Francesco Lamanna francesco.lamanna at gmail.com
Thu Jan 11 12:28:43 GMT 2018


Hi Mateus,

if I try to initialize the LoadMemebers pipeline without “--collection
ensembl”, I get the following error:

The following options are missing:
    {'collection'}

I also tried to set 'collection' => undef, in the conf file, but I get
another error:

The master dabase must be defined with a collection at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/PipeConfig/LoadMembers_conf.pm
line 190.

Cheers,
Francesco

2018-01-11 12:01 GMT+01:00 Mateus Patricio <mateus at ebi.ac.uk>:

> 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>:
>
>> 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::PipeCon
>> fig::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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