[ensembl-dev] Problem with genome_member_copy (Compara).
Matthieu Muffato
muffato at ebi.ac.uk
Fri Jan 12 16:48:29 GMT 2018
Hi Francesco
Homoeologues are only used when running on plant genomes (which have
polyploid genomes), but the pipeline configuration is shared and expects
this method_link to be present
This how it looks in the Ensembl Plants database. You can insert this
row in your database and it should work
ensro at mysql-eg-publicsql.ebi.ac.uk:4157/ensembl_compara_plants_38_91
[Fri Jan 12 16:46:32 2018] > SELECT * FROM method_link WHERE
method_link_id = 206;
+----------------+----------------------+-------------------+
| method_link_id | type | class |
+----------------+----------------------+-------------------+
| 206 | ENSEMBL_HOMOEOLOGUES | Homology.homology |
+----------------+----------------------+-------------------+
Regards,
Matthieu
On 12/01/18 14:01, Francesco Lamanna wrote:
> 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 <mailto: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
> <mailto: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
>> <mailto: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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--
Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room A3-145
Phone + 44 (0) 1223 49 4631
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