[ensembl-dev] Problem with genome_member_copy (Compara).
Francesco Lamanna
francesco.lamanna at gmail.com
Mon Jan 15 17:53:15 GMT 2018
Hi Matthieu,
your suggestion solves this particular problem, but it looks that it messes
up the next step:
Database changed
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 18:38:31 | 0 | WRITE_OUTPUT |
Successfully copied 1646504 'ncbi_taxa_node'
rows
| 0 |
| 9 | copy_ncbi_table | 2 | 6
| 4 | 4 | 2018-01-15 18:41:47 | 0 | WRITE_OUTPUT |
Successfully copied 2504391 'ncbi_taxa_name'
rows
| 0 |
| 10 | populate_method_links_from_db | 3 | 7
| 6 | 6 | 2018-01-15 18:43:04 | 0 | WRITE_OUTPUT |
Successfully copied 19 'method_link'
rows
| 0 |
| 16 | create_mlss_ss | 4 | 10
| 9 | 9 | 2018-01-15 18:46:08 | 0 | WRITE_OUTPUT | The
Method dbID=401 'PROTEIN_TREES', class='ProteinTree.protein_tree_node' /
SpeciesSet dbID=17 "empty"', genome_dbs=[] [unreleased]
MethodLinkSpeciesSet could not be found in the master database | 1 |
| 16 | create_mlss_ss | 5 | 10
| 10 | 10 | 2018-01-15 18:47:10 | 1 | WRITE_OUTPUT | The
Method dbID=401 'PROTEIN_TREES', class='ProteinTree.protein_tree_node' /
SpeciesSet dbID=17 "empty"', genome_dbs=[] [unreleased]
MethodLinkSpeciesSet could not be found in the master database | 1 |
| 16 | create_mlss_ss | 6 | 10
| 11 | 11 | 2018-01-15 18:48:10 | 2 | WRITE_OUTPUT | The
Method dbID=401 'PROTEIN_TREES', class='ProteinTree.protein_tree_node' /
SpeciesSet dbID=17 "empty"', genome_dbs=[] [unreleased]
MethodLinkSpeciesSet could not be found in the master database | 1 |
| 16 | create_mlss_ss | 7 | 10
| 12 | 12 | 2018-01-15 18:49:12 | 3 | WRITE_OUTPUT | The
Method dbID=401 'PROTEIN_TREES', class='ProteinTree.protein_tree_node' /
SpeciesSet dbID=17 "empty"', genome_dbs=[] [unreleased]
MethodLinkSpeciesSet could not be found in the master database | 1 |
+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
7 rows in set (0.01 sec)
Cheers,
Francesco.
2018-01-15 17:52 GMT+01:00 muffato <muffato at ebi.ac.uk>:
> Hi there,
>
> I think I know what's going on. See there are two spaces between between
> "The" and "species-set" in "The species-set could not be found in the
> master database" ? There is supposed to be the content of the set there,
> but it's an empty string. Probably because the species-set it needs to use
> is actually empty. In other words, the pipeline may be requiring an empty
> species-set to be in the master database too. Give it a try by creating a
> new row in species_set_header with (17, 'empty', 0, NULL, NULL) and
> rerunning the job
>
> Matthieu
>
> On 2018-01-15 16:28, Wasiu Akanni wrote:
>
>> I would suggest setting the first release to the ensembl code version
>> that you are using.
>>
>> On 15/01/2018 16:22, Francesco Lamanna wrote:
>>
>> Hi Wasiu,
>>>
>>> this is the output of the species_set_header table:
>>>
>>> mysql> SELECT * FROM species_set_header;
>>>
>>> +----------------+-------------------------------+------+---
>> ------------+--------------+
>>
>>> | species_set_id | name | size |
>>> first_release | last_release |
>>>
>>> +----------------+-------------------------------+------+---
>> ------------+--------------+
>>
>>> | 1 | H.sap-G.gal | 2 |
>>> NULL | NULL |
>>> | 2 | H.sap-B.flo | 2 |
>>> NULL | NULL |
>>> | 3 | H.sap-P.mar | 2 |
>>> NULL | NULL |
>>> | 4 | H.sap-C.mil [1] | 2 |
>>> NULL | NULL |
>>> | 5 | G.gal-B.flo | 2 |
>>> NULL | NULL |
>>> | 6 | G.gal-P.mar | 2 |
>>> NULL | NULL |
>>> | 7 | G.gal-C.mil [2] | 2 |
>>> NULL | NULL |
>>> | 8 | B.flo-P.mar | 2 |
>>> NULL | NULL |
>>> | 9 | B.flo-C.mil [3] | 2 |
>>> NULL | NULL |
>>> | 10 | P.mar-C.mil [4] | 2 |
>>> NULL | NULL |
>>> | 11 | H.sap | 1 |
>>> NULL | NULL |
>>> | 12 | G.gal | 1 |
>>> NULL | NULL |
>>> | 13 | B.flo | 1 |
>>> NULL | NULL |
>>> | 14 | P.mar | 1 |
>>> NULL | NULL |
>>> | 15 | C.mil | 1 |
>>> NULL | NULL |
>>> | 16 | H.sap-G.gal-B.flo-P.mar-C.mil [5] | 5 |
>>> NULL | NULL |
>>>
>>> +----------------+-------------------------------+------+---
>> ------------+--------------+
>>
>>> 16 rows in set (0.05 sec)
>>>
>>> It looks ok
>>>
>>> 2018-01-15 17:19 GMT+01:00 Wasiu Akanni <waakanni at ebi.ac.uk>:
>>>
>>> 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>:
>>> 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
>>> [6] [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 [7] <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.
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> <mailto:Dev at ensembl.org>
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev [8]
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>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> <mailto:Dev at ensembl.org>
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>>>
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>>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
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>>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info:
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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 [9]
>> Fax + 44 (0) 1223 49 4468 [10]
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev [8]
>> Ensembl Blog: http://www.ensembl.info/
>>
>> --
>> WASIU AJENIFUJA AKANNI
>> Developer
>>
>> Compara group
>> EMBL-EBI
>> Phone: + 44 (0) 1223 494 237 [11]
>> Room A3145, West building | Wellcome Trust Genome Campus | Hinxton |
>> Cambridge | CB10 1SD | UK
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev [8]
>> Ensembl Blog: http://www.ensembl.info/
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>> --
>> 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
>>
>> Links:
>> ------
>> [1] http://H.sap-C.mil
>> [2] http://G.gal-C.mil
>> [3] http://B.flo-C.mil
>> [4] http://P.mar-C.mil
>> [5] http://H.sap-G.gal-B.flo-P.mar-C.mil
>> [6] http://ensro@mysql-eg-publicsql.ebi.ac.uk:4157/ensembl_
>> compara_plants_38_91
>> [7] http://init_pipeline.pl
>> [8] http://lists.ensembl.org/mailman/listinfo/dev
>> [9] tel:%2B%2044%20%280%29%201223%2049%204631
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