[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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