[ensembl-dev] Problem with genome_member_copy (Compara).
Wasiu Akanni
waakanni at ebi.ac.uk
Mon Jan 15 16:19:00 GMT 2018
Hi Francesco,
Have you checked the species_set_header table?
On 15/01/2018 14:39, Francesco Lamanna wrote:
> Hi Matthieu,
>
> thank you for your suggestion, it fixed the problem.
>
> However, I still 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 |
> +-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------+----------+
> | 9 | copy_ncbi_table | 1 | 5 | 3
> | 3 | 2018-01-15 14:49:29 | 0 | WRITE_OUTPUT |
> Successfully copied 1646504 'ncbi_taxa_node' rows | 0 |
> | 9 | copy_ncbi_table | 2 | 6 | 4
> | 4 | 2018-01-15 14:50:36 | 0 | WRITE_OUTPUT |
> Successfully copied 2504391 'ncbi_taxa_name' rows | 0 |
> | 10 | populate_method_links_from_db | 3 |
> 7 | 6 | 6 | 2018-01-15 14:52:06 | 0 | WRITE_OUTPUT |
> Successfully copied 19 'method_link' rows | 0 |
> | 16 | create_mlss_ss | 4 | 10 | 9
> | 9 | 2018-01-15 14:55:10 | 0 | WRITE_OUTPUT | The
> species-set could not be found in the master database | 1 |
> | 16 | create_mlss_ss | 5 | 10 | 10
> | 10 | 2018-01-15 14:56:11 | 1 | WRITE_OUTPUT | The
> species-set could not be found in the master database | 1 |
> | 16 | create_mlss_ss | 6 | 10 | 11
> | 11 | 2018-01-15 14:57:12 | 2 | WRITE_OUTPUT | The
> species-set could not be found in the master database | 1 |
> | 16 | create_mlss_ss | 7 | 10 | 12
> | 12 | 2018-01-15 14:58:21 | 3 | WRITE_OUTPUT | The
> species-set could not be found in the master database | 1 |
> +-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------+----------+
> 7 rows in set (0.01 sec)
>
> But my species_set in the master_db is not empty:
>
> mysql> SELECT * FROM species_set;
> +----------------+--------------+
> | species_set_id | genome_db_id |
> +----------------+--------------+
> | 1 | 1 |
> | 1 | 2 |
> | 2 | 1 |
> | 2 | 3 |
> | 3 | 1 |
> | 3 | 4 |
> | 4 | 1 |
> | 4 | 5 |
> | 5 | 2 |
> | 5 | 3 |
> | 6 | 2 |
> | 6 | 4 |
> | 7 | 2 |
> | 7 | 5 |
> | 8 | 3 |
> | 8 | 4 |
> | 9 | 3 |
> | 9 | 5 |
> | 10 | 4 |
> | 10 | 5 |
> | 11 | 1 |
> | 12 | 2 |
> | 13 | 3 |
> | 14 | 4 |
> | 15 | 5 |
> | 16 | 1 |
> | 16 | 2 |
> | 16 | 3 |
> | 16 | 4 |
> | 16 | 5 |
> +----------------+--------------+
> 30 rows in set (0.00 sec)
>
> I am quite puzzled by this error.
>
> Cheers,
> Francesco.
>
> 2018-01-12 17:48 GMT+01:00 Matthieu Muffato <muffato at ebi.ac.uk
> <mailto:muffato at ebi.ac.uk>>:
>
> 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
> <http://ensro@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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <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>
> <mailto: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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> --
> 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
> <tel:%2B%2044%20%280%29%201223%2049%204631>
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--
*Wasiu Ajenifuja Akanni*
Developer
Compara group
EMBL-EBI
Phone: + 44 (0) 1223 494 237
Room A3145, West building | Wellcome Trust Genome Campus | Hinxton |
Cambridge | CB10 1SD | UK
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