<div dir="ltr"><div><div>Hi Wasiu,<br><br></div>this is the output of the species_set_header table:<br><br>mysql> SELECT * FROM species_set_header;<br>+----------------+-------------------------------+------+---------------+--------------+<br>| species_set_id | name                          | size | first_release | last_release |<br>+----------------+-------------------------------+------+---------------+--------------+<br>|              1 | H.sap-G.gal                   |    2 |          NULL |         NULL |<br>|              2 | H.sap-B.flo                   |    2 |          NULL |         NULL |<br>|              3 | H.sap-P.mar                   |    2 |          NULL |         NULL |<br>|              4 | <a href="http://H.sap-C.mil">H.sap-C.mil</a>                   |    2 |          NULL |         NULL |<br>|              5 | G.gal-B.flo                   |    2 |          NULL |         NULL |<br>|              6 | G.gal-P.mar                   |    2 |          NULL |         NULL |<br>|              7 | <a href="http://G.gal-C.mil">G.gal-C.mil</a>                   |    2 |          NULL |         NULL |<br>|              8 | B.flo-P.mar                   |    2 |          NULL |         NULL |<br>|              9 | <a href="http://B.flo-C.mil">B.flo-C.mil</a>                   |    2 |          NULL |         NULL |<br>|             10 | <a href="http://P.mar-C.mil">P.mar-C.mil</a>                   |    2 |          NULL |         NULL |<br>|             11 | H.sap                         |    1 |          NULL |         NULL |<br>|             12 | G.gal                         |    1 |          NULL |         NULL |<br>|             13 | B.flo                         |    1 |          NULL |         NULL |<br>|             14 | P.mar                         |    1 |          NULL |         NULL |<br>|             15 | C.mil                         |    1 |          NULL |         NULL |<br>|             16 | <a href="http://H.sap-G.gal-B.flo-P.mar-C.mil">H.sap-G.gal-B.flo-P.mar-C.mil</a> |    5 |          NULL |         NULL |<br>+----------------+-------------------------------+------+---------------+--------------+<br>16 rows in set (0.05 sec)<br><br></div>It looks ok<br></div><div class="gmail_extra"><br><div class="gmail_quote">2018-01-15 17:19 GMT+01:00 Wasiu Akanni <span dir="ltr"><<a href="mailto:waakanni@ebi.ac.uk" target="_blank">waakanni@ebi.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div text="#000000" bgcolor="#FFFFFF">
    <p>Hi Francesco,</p>
    <p>Have you checked the species_set_header table?<br>
    </p><div><div class="h5">
    <br>
    <div class="m_-2801295335211067424moz-cite-prefix">On 15/01/2018 14:39, Francesco Lamanna
      wrote:<br>
    </div>
    <blockquote type="cite">
      <div dir="ltr">
        <div>
          <div>
            <div>
              <div>
                <div>
                  <div>Hi Matthieu,<br>
                    <br>
                  </div>
                  thank you for your suggestion, it fixed the problem.<br>
                  <br>
                </div>
                However, I still get the following error:<br>
                <br>
                mysql> SELECT * FROM msg;<br>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>--------------------+---------<wbr>-+<br>
                | analysis_id | logic_name                    |
                log_message_id | job_id | role_id | worker_id |
                when_logged         | retry | status       |
                msg                           <wbr>                            
                | is_error |<br>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>--------------------+---------<wbr>-+<br>
                |           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 |<br>
                |           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 |<br>
                |          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 |<br>
                |          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 |<br>
                |          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 |<br>
                |          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 |<br>
                |          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 |<br>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>--------------------+---------<wbr>-+<br>
                7 rows in set (0.01 sec)<br>
                <br>
              </div>
              But my species_set in the master_db is not empty:<br>
              <br>
              mysql> SELECT * FROM species_set;<br>
              +----------------+------------<wbr>--+<br>
              | species_set_id | genome_db_id |<br>
              +----------------+------------<wbr>--+<br>
              |              1 |            1 |<br>
              |              1 |            2 |<br>
              |              2 |            1 |<br>
              |              2 |            3 |<br>
              |              3 |            1 |<br>
              |              3 |            4 |<br>
              |              4 |            1 |<br>
              |              4 |            5 |<br>
              |              5 |            2 |<br>
              |              5 |            3 |<br>
              |              6 |            2 |<br>
              |              6 |            4 |<br>
              |              7 |            2 |<br>
              |              7 |            5 |<br>
              |              8 |            3 |<br>
              |              8 |            4 |<br>
              |              9 |            3 |<br>
              |              9 |            5 |<br>
              |             10 |            4 |<br>
              |             10 |            5 |<br>
              |             11 |            1 |<br>
              |             12 |            2 |<br>
              |             13 |            3 |<br>
              |             14 |            4 |<br>
              |             15 |            5 |<br>
              |             16 |            1 |<br>
              |             16 |            2 |<br>
              |             16 |            3 |<br>
              |             16 |            4 |<br>
              |             16 |            5 |<br>
              +----------------+------------<wbr>--+<br>
              30 rows in set (0.00 sec)<br>
              <br>
            </div>
            I am quite puzzled by this error.<br>
            <br>
          </div>
          Cheers,<br>
        </div>
        Francesco.<br>
      </div>
      <div class="gmail_extra"><br>
        <div class="gmail_quote">2018-01-12 17:48 GMT+01:00 Matthieu
          Muffato <span dir="ltr"><<a href="mailto:muffato@ebi.ac.uk" target="_blank">muffato@ebi.ac.uk</a>></span>:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi
            Francesco<br>
            <br>
            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<br>
            <br>
            This how it looks in the Ensembl Plants database. You can
            insert this row in your database and it should work<br>
            <br>
            <a href="http://ensro@mysql-eg-publicsql.ebi.ac.uk:4157/ensembl_compara_plants_38_91" rel="noreferrer" target="_blank">ensro@mysql-eg-publicsql.ebi.a<wbr>c.uk:4157/ensembl_compara_plan<wbr>ts_38_91</a>
            [Fri Jan 12 16:46:32 2018] > SELECT * FROM method_link
            WHERE method_link_id = 206;<br>
            +----------------+------------<wbr>----------+-------------------<wbr>+<br>
            | method_link_id | type                 | class           
             |<br>
            +----------------+------------<wbr>----------+-------------------<wbr>+<br>
            |            206 | ENSEMBL_HOMOEOLOGUES | Homology.homology
            |<br>
            +----------------+------------<wbr>----------+-------------------<wbr>+<br>
            <br>
            Regards,<br>
            Matthieu<span><br>
              <br>
              On 12/01/18 14:01, Francesco Lamanna wrote:<br>
            </span>
            <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span>
                Hi Mateus,<br>
                <br>
                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');"<br>
                <br>
                in LoadMembers_conf.pm. The member_db is now correctly
                set up.<br>
                <br>
                However, when I run the Protein trees pipeline I get the
                following error message<br>
                <br>
                mysql> SELECT * FROM msg;<br>
                +-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-----------------+----------+<br>
                | analysis_id | logic_name                    |
                log_message_id | job_id | role_id | worker_id |
                when_logged         | retry | status       | msg       
                                                                       
                                                                       
                                                                     |
                is_error |<br>
                +-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-----------------+----------+<br>
                |           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 |<br>
                |           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 |<br>
                |          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 |<br>
                |          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/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm
                line 70. |        1 |<br>
                |          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/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm
                line 70. |        1 |<br>
                |          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/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm
                line 70. |        1 |<br>
                |          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/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm
                line 70. |        1 |<br>
                |          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/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm
                line 70. |        1 |<br>
                +-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-----------------+----------+<br>
                8 rows in set (0.01 sec)<br>
                <br>
                I wasn't aware about this method_link.<br>
                <br>
                Do you know how can I fix this?<br>
                <br>
                Thanks,<br>
                Francesco.<br>
                <br>
              </span>
              2018-01-11 13:28 GMT+01:00 Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a>
              <mailto:<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmai<wbr>l.com</a>>>:<span><br>
                <br>
                    Hi Mateus,<br>
                <br>
                    if I try to initialize the LoadMemebers pipeline
                without<br>
                    “--collection ensembl”, I get the following error:<br>
                <br>
                    The following options are missing:<br>
                         {'collection'}<br>
                <br>
                    I also tried to set 'collection' => undef, in the
                conf file, but I<br>
                    get another error:<br>
                <br>
                    The master dabase must be defined with a collection
                at<br>
                    /home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/PipeConfig/Loa<wbr>dMembers_conf.pm<br>
                    line 190.<br>
                <br>
                    Cheers,<br>
                    Francesco<br>
                <br>
                    2018-01-11 12:01 GMT+01:00 Mateus Patricio <<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a><br>
              </span>
                  <mailto:<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a>>>:<span><br>
                <br>
                        Hi Francesco,<br>
                <br>
                        In your case the solution should be starting the
                LoadMembers<br>
                        without the option “--collection ensembl”.<br>
                <br>
                        If you start the pipeline without it, it should
                use all the<br>
                        current species in your master database.<br>
                <br>
                        In Ensembl we have different collections that
                are used for<br>
                        different purposes, and the default one is
                “ensembl”.<br>
                <br>
                        Please let me know if this works.<br>
                <br>
                        Cheers,<br>
                <br>
                        Mateus.<br>
                <br>
                <br>
              </span>
              <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span>
                          On 11 Jan 2018, at 10:13, Francesco Lamanna<br>
                          <<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a><br>
                </span>
                <div>
                  <div class="m_-2801295335211067424h5">
                            <mailto:<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmai<wbr>l.com</a>>>
                    wrote:<br>
                    <br>
                            Hi Mateus,<br>
                    <br>
                            many thanks for your answer.<br>
                    <br>
                            I am trying to launch the LoadMembers
                    pipeline in order to<br>
                            make a member_db, but I get the following
                    error:<br>
                    <br>
                            mysql> SELECT * from msg;<br>
                            +-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-+----------+<br>
                            | analysis_id | logic_name             |
                    log_message_id |<br>
                            job_id | role_id | worker_id |
                    when_logged         | retry |<br>
                            status       | msg                  |
                    is_error |<br>
                            +-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-+----------+<br>
                            |           3 | copy_table_from_master
                    |              1 |             4 |       3 |        
                    3 | 2018-01-11 11:04:02 |     0 |<br>
                            WRITE_OUTPUT | Successfully copied 1646504
                    'ncbi_taxa_node'<br>
                            rows   |        0 |<br>
                            |           3 | copy_table_from_master
                    |              2 |             5 |       4 |        
                    4 | 2018-01-11 11:05:46 |     0 |<br>
                            WRITE_OUTPUT | Successfully copied 2504391
                    'ncbi_taxa_name'<br>
                            rows   |        0 |<br>
                            |           4 | load_genomedb_factory 
                    |              3 |             3 |       5 |        
                    5 | 2018-01-11 11:07:06 |     0 |<br>
                            FETCH_INPUT  | Could not fetch collection ss
                    with name=ensembl<br>
                            at<br>
                            /home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Gen<wbr>omeDBFactory.pm<br>
                            line 106. |        1 |<br>
                            |           4 | load_genomedb_factory 
                    |              4 |             3 |       6 |        
                    6 | 2018-01-11 11:08:00 |     1 |<br>
                            FETCH_INPUT  | Could not fetch collection ss
                    with name=ensembl<br>
                            at<br>
                            /home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Gen<wbr>omeDBFactory.pm<br>
                            line 106. |        1 |<br>
                            |           4 | load_genomedb_factory 
                    |              5 |             3 |       7 |        
                    7 | 2018-01-11 11:08:25 |     2 |<br>
                            FETCH_INPUT  | Could not fetch collection ss
                    with name=ensembl<br>
                            at<br>
                            /home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Gen<wbr>omeDBFactory.pm<br>
                            line 106. |        1 |<br>
                            |           4 | load_genomedb_factory 
                    |              6 |             3 |       8 |        
                    8 | 2018-01-11 11:09:25 |     3 |<br>
                            FETCH_INPUT  | Could not fetch collection ss
                    with name=ensembl<br>
                            at<br>
                            /home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Gen<wbr>omeDBFactory.pm<br>
                            line 106. |        1 |<br>
                            +-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-+----------+<br>
                            6<br>
                    <br>
                            Cheers,<br>
                            Francesco.<br>
                    <br>
                            2018-01-10 17:31 GMT+01:00 Mateus Patricio
                    <<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a><br>
                  </div>
                </div>
                        <mailto:<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a>>>:<span><br>
                  <br>
                              Hi Francesco<br>
                  <br>
                              The protein tree pipeline reuses the genes
                  and sequence<br>
                              members from the 'reuse_db' parameter,
                  which in this case<br>
                              should point to a members database.<br>
                  <br>
                              This members database can be created by
                  running the<br>
                              LoadMembers pipeline.<br>
                  <br>
                              You can initiate the pipeline with the
                  following command line:<br>
                  <br>
                </span>
                            <a href="http://init_pipeline.pl" rel="noreferrer" target="_blank">init_pipeline.pl</a> <<a href="http://init_pipeline.pl/" rel="noreferrer" target="_blank">http://init_pipeline.pl/</a>><span><br>
                              Bio::EnsEMBL::Compara::PipeCon<wbr>fig::EBI::Ensembl::LoadMembers<wbr>_conf<br>
                              --collection ensembl<br>
                  <br>
                              Then you should point the parameter
                  reuse_db to this<br>
                              database on your Protein Tree config file.<br>
                  <br>
                              'reuse_db'   =>
                  'mysql://ensro@host:port/datab<wbr>ase',<br>
                  <br>
                              Please do let me know if you have further
                  questions.<br>
                  <br>
                              Cheers,<br>
                  <br>
                              Mateus.<br>
                  <br>
                  <br>
                </span>
                <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span>
                                On 10 Jan 2018, at 16:06, Francesco
                    Lamanna<br>
                                <<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a><br>
                  </span>
                  <div>
                    <div class="m_-2801295335211067424h5">
                                  <mailto:<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmai<wbr>l.com</a>>>
                      wrote:<br>
                      <br>
                                  Hi all,<br>
                      <br>
                                  when I try to run the protein tree
                      pipeline (v91) using<br>
                                  the core Human and Chicken genomes I
                      get the following<br>
                                  error message:<br>
                      <br>
                                  mysql> SELECT * from msg;<br>
                                  +-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br>
                                  | analysis_id |
                      logic_name                    |<br>
                                  log_message_id | job_id | role_id |
                      worker_id |<br>
                                  when_logged         | retry |
                      status       | msg<br>
                                                         | is_error |<br>
                                  +-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br>
                                  |           9 | copy_ncbi_table       
                                        |              1 |      5
                      |       3 |         4 |<br>
                                  2018-01-10 16:40:13 |     0 |
                      WRITE_OUTPUT | Successfully<br>
                                  copied 1646504 'ncbi_taxa_node' rows
                              |        0 |<br>
                                  |           9 | copy_ncbi_table       
                                        |              2 |      6
                      |       4 |         3 |<br>
                                  2018-01-10 16:42:04 |     0 |
                      WRITE_OUTPUT | Successfully<br>
                                  copied 2504391 'ncbi_taxa_name' rows
                              |        0 |<br>
                                  |          10 |
                      populate_method_links_from_db<br>
                                  |              3 |      7 |       6
                      |         6 |<br>
                                  2018-01-10 16:43:44 |     0 |
                      WRITE_OUTPUT | Successfully<br>
                                  copied 18 'method_link' rows
                                      |        0 |<br>
                                  |          25 | genome_member_copy   
                                         |              4 |     13
                      |      11 |        11 |<br>
                                  2018-01-10 16:47:49 |     0 |
                      FETCH_INPUT  | ParamError:<br>
                                  value for param_required('reuse_db')
                      is required and has<br>
                                  to be defined |        1 |<br>
                                  |          25 | genome_member_copy   
                                         |              5 |     14
                      |      12 |        12 |<br>
                                  2018-01-10 16:47:49 |     0 |
                      FETCH_INPUT  | ParamError:<br>
                                  value for param_required('reuse_db')
                      is required and has<br>
                                  to be defined |        1 |<br>
                                  +-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br>
                      <br>
                                  I have no clue about what to put in
                      the 'reuse_db'<br>
                                  parameter (nor could I find any
                      information in the<br>
                                  compara docs).<br>
                      <br>
                                  Can anyone please help me to solve
                      this issue?<br>
                      <br>
                                  Thanks,<br>
                                  Francesco.<br>
                                  ______________________________<wbr>_________________<br>
                    </div>
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                  </span></blockquote>
                <br>
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                <br>
                <br>
                <br>
                <br>
                <br>
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                <br>
              </span></blockquote>
            <span class="m_-2801295335211067424HOEnZb"><font color="#888888">
                <br>
                -- <br>
                Matthieu Muffato, Ph.D.<br>
                Ensembl Compara and TreeFam Project Leader<br>
                European Bioinformatics Institute (EMBL-EBI)<br>
                European Molecular Biology Laboratory<br>
                Wellcome Trust Genome Campus, Hinxton<br>
                Cambridge, CB10 1SD, United Kingdom<br>
                Room  A3-145<br>
                Phone <a href="tel:%2B%2044%20%280%29%201223%2049%204631" value="+441223494631" target="_blank">+ 44 (0) 1223 49 4631</a><br>
                Fax   <a href="tel:%2B%2044%20%280%29%201223%2049%204468" value="+441223494468" target="_blank">+ 44 (0) 1223 49 4468</a><br>
              </font></span></blockquote>
        </div>
        <br>
      </div>
      <br>
      <fieldset class="m_-2801295335211067424mimeAttachmentHeader"></fieldset>
      <br>
      <pre>______________________________<wbr>_________________
Dev mailing list    <a class="m_-2801295335211067424moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
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</pre>
    </blockquote>
    <br>
    </div></div><span class="HOEnZb"><font color="#888888"><div class="m_-2801295335211067424moz-signature">-- <br>
      <b><big>Wasiu Ajenifuja Akanni</big></b><br>
      Developer<br>
      <br>
      Compara group<br>
      EMBL-EBI<br>
      Phone: <a href="tel:+44%201223%20494237" value="+441223494237" target="_blank">+ 44 (0) 1223 494 237</a><br>
      Room A3145, West building | Wellcome Trust Genome Campus | Hinxton
      | Cambridge | CB10 1SD | UK</div>
  </font></span></div>

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<br></blockquote></div><br></div>