[ensembl-dev] Problem with genome_member_copy (Compara).
Francesco Lamanna
francesco.lamanna at gmail.com
Fri Jan 12 14:01:57 GMT 2018
Hi Mateus,
I could solve this problem by commenting out the line: "die "The master
dabase must be defined with a collection" if $self->o('master_db') and not
$self->o('collection');"
in LoadMembers_conf.pm. The member_db is now correctly set up.
However, when I run the Protein trees pipeline 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 | 3 | 2018-01-12 14:21:39 | 0 | WRITE_OUTPUT |
Successfully copied 1646504 'ncbi_taxa_node'
rows
| 0 |
| 9 | copy_ncbi_table | 2 | 6
| 4 | 4 | 2018-01-12 14:25:27 | 0 | WRITE_OUTPUT |
Successfully copied 2504391 'ncbi_taxa_name'
rows
| 0 |
| 10 | populate_method_links_from_db | 3 | 7
| 6 | 6 | 2018-01-12 14:26:54 | 0 | WRITE_OUTPUT |
Successfully copied 18 'method_link'
rows
| 0 |
| 16 | create_mlss_ss | 4 | 10
| 9 | 9 | 2018-01-12 14:29:56 | 0 | FETCH_INPUT | Cannot
find the method_link 'ENSEMBL_HOMOEOLOGUES' at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/PrepareSpeciesSetsMLSS.pm
line 70. | 1 |
| 16 | create_mlss_ss | 5 | 10
| 10 | 10 | 2018-01-12 14:30:57 | 1 | FETCH_INPUT | Cannot
find the method_link 'ENSEMBL_HOMOEOLOGUES' at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/PrepareSpeciesSetsMLSS.pm
line 70. | 1 |
| 16 | create_mlss_ss | 6 | 10
| 11 | 11 | 2018-01-12 14:31:58 | 2 | FETCH_INPUT | Cannot
find the method_link 'ENSEMBL_HOMOEOLOGUES' at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/PrepareSpeciesSetsMLSS.pm
line 70. | 1 |
| 16 | create_mlss_ss | 7 | 10
| 12 | 12 | 2018-01-12 14:33:00 | 3 | FETCH_INPUT | Cannot
find the method_link 'ENSEMBL_HOMOEOLOGUES' at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/PrepareSpeciesSetsMLSS.pm
line 70. | 1 |
| 16 | create_mlss_ss | 8 | 10
| 13 | 13 | 2018-01-12 14:38:36 | 1 | FETCH_INPUT | Cannot
find the method_link 'ENSEMBL_HOMOEOLOGUES' at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/PrepareSpeciesSetsMLSS.pm
line 70. | 1 |
+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
8 rows in set (0.01 sec)
I wasn't aware about this method_link.
Do you know how can I fix this?
Thanks,
Francesco.
2018-01-11 13:28 GMT+01:00 Francesco Lamanna <francesco.lamanna at gmail.com>:
> 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/EnsEMB
>> L/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/EnsEMB
>> L/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/EnsEMB
>> L/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/EnsEMB
>> L/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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