[ensembl-dev] Problem with genome_member_copy (Compara).
Francesco Lamanna
francesco.lamanna at gmail.com
Thu Jan 11 10:13:44 GMT 2018
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::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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