<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Francesco,<div class=""><br class=""></div><div class="">Could you please confirm which checkout version of the compara code you have?</div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Mateus.</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 13 Nov 2017, at 10:50, Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" class="">francesco.lamanna@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class="">Hi Mateus and Brandon,<br class=""><br class=""></div>many thanks for your patch, it solved the issue.<br class=""><br class=""></div>Unfortunately, I got stuck at the successive step with the following error message:<br class=""><br class="">mysql> SELECT * FROM msg;<br class="">+-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br class="">| analysis_id | logic_name                 | log_message_id | job_id | role_id | worker_id | when_logged         | retry | status       | msg                                                                                                                                                                      | is_error |<br class="">+-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br class="">|           9 | copy_ncbi_table            |              1 |      5 |       3 |         3 | 2017-11-13 11:16:31 |     0 | WRITE_OUTPUT | Successfully copied 1609518 'ncbi_taxa_node' rows                                                                                                                        |        0 |<br class="">|           9 | copy_ncbi_table            |              2 |      6 |       4 |         4 | 2017-11-13 11:20:15 |     0 | WRITE_OUTPUT | Successfully copied 2438889 'ncbi_taxa_name' rows                                                                                                                        |        0 |<br class="">|          18 | make_treebest_species_tree |              3 |     10 |       9 |         9 | 2017-11-13 11:25:29 |     0 | FETCH_INPUT  | Can't call method "get_all_subnodes" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. |        1 |<br class="">|          18 | make_treebest_species_tree |              4 |     10 |      11 |        11 | 2017-11-13 11:26:29 |     1 | FETCH_INPUT  | Can't call method "get_all_subnodes" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. |        1 |<br class="">|          18 | make_treebest_species_tree |              5 |     10 |      13 |        13 | 2017-11-13 11:27:31 |     2 | FETCH_INPUT  | Can't call method "get_all_subnodes" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. |        1 |<br class="">|          18 | make_treebest_species_tree |              6 |     10 |      16 |        16 | 2017-11-13 11:28:32 |     3 | FETCH_INPUT  | Can't call method "get_all_subnodes" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. |        1 |<br class="">+-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br class="">6 rows in set (0.00 sec)<br class=""><br class=""></div>Do you have any suggestion?<br class=""><br class=""></div>Thanks,<br class=""></div>Francesco<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2017-11-09 17:25 GMT+01:00 Brandon Walts <span dir="ltr" class=""><<a href="mailto:bwalts@ebi.ac.uk" target="_blank" class="">bwalts@ebi.ac.uk</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div text="#000000" bgcolor="#FFFFFF" class=""><p class="">Hi Francesco</p><p class="">We have just pushed a fix to the MySQLTransfer.pm runnable, so
      that it no longer locks tables by default. If you go to your eHive
      checkout and perform a git pull, you should get this fix. <br class="">
    </p><p class="">Users who wish to retain the table locking behavior can switch it
      on by passing a parameter 'lock_tables=1' to MySQLTransfer.pm</p><p class="">Best<span class="HOEnZb"><font color="#888888" class=""><br class="">
      -Brandon<br class="">
    </font></span></p><div class=""><div class="h5">
    <br class="">
    <div class="m_936139081383433000moz-cite-prefix">On 09/11/2017 16:20, Mateus Patricio
      wrote:<br class="">
    </div>
    <blockquote type="cite" class="">
      
      <div class="">Hi Francesco,</div>
      <div class=""><br class="">
      </div>
      <div class="">So what’s happening here is that you are trying to
        lock a table in one of our servers.</div>
      <div class=""><br class="">
      </div>
      <div class="">That can be fixed by telling mysqldump to avoid
        locking the table. (Like you initially suspected)</div>
      <div class=""><br class="">
      </div>
      <div class="">You could do that directly on the eHive runnable
        "ehive/master/modules/Bio/<wbr class="">EnsEMBL/Hive/RunnableDB/<wbr class="">MySQLTransfer.pm”</div>
      <div class=""><br class="">
      </div>
      <div class="">The dump command is constructed at:</div>
      <div class=""><a href="https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117" target="_blank" class="">https://github.com/Ensembl/<wbr class="">ensembl-hive/blob/<wbr class="">6c4877d4eda1bf0469c29bdbe58932<wbr class="">671848cc20/modules/Bio/<wbr class="">EnsEMBL/Hive/RunnableDB/<wbr class="">MySQLTransfer.pm#L117</a></div>
      <div class=""><br class="">
      </div>
      <div class="">I would suggest you to create a new entry to
        “mode_options”:</div>
      <div class=""><a href="https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112" target="_blank" class="">https://github.com/Ensembl/<wbr class="">ensembl-hive/blob/<wbr class="">6c4877d4eda1bf0469c29bdbe58932<wbr class="">671848cc20/modules/Bio/<wbr class="">EnsEMBL/Hive/RunnableDB/<wbr class="">MySQLTransfer.pm#L112</a></div>
      <div class=""><br class="">
      </div>
      <div class="">So that you could access directly from your pipeline
        config file, by setting something like:</div>
      <div class="">
        <div class=""><br class="">
        </div>
      </div>
      <blockquote type="cite" class="">
        <div class="">
          <div class=""><font face="Courier New" class="">        {  
              -logic_name    => 'copy_ncbi_table',</font></div>
          <div class=""><font face="Courier New" class="">           
              -module        =>
              'Bio::EnsEMBL::Hive::<wbr class="">RunnableDB::MySQLTransfer',</font></div>
          <div class=""><font face="Courier New" class="">           
              -parameters    => {</font></div>
          <div class=""><font face="Courier New" class="">             
                'src_db_conn'   => '#ncbi_db#',</font></div>
          <div class=""><font face="Courier New" class="">             
                'mode'          => ’<b class="">SKIP_LOCK</b>',</font></div>
          <div class=""><font face="Courier New" class="">             
                'filter_cmd'    => 'sed
              "s/ENGINE=MyISAM/ENGINE=<wbr class="">InnoDB/"',</font></div>
          <div class=""><font face="Courier New" class="">            },</font></div>
          <div class=""><font face="Courier New" class="">        },</font></div>
        </div>
      </blockquote>
      <div class=""><br class="">
      </div>
      <div class="">Please let me know if that doesn’t work.</div>
      <div class=""><br class="">
      </div>
      <div class="">Cheers,</div>
      <div class=""><br class="">
      </div>
      <div class="">Mateus.</div>
      <div class=""><br class="">
      </div>
      <div class=""><br class="">
        <div class=""><br class="">
        </div>
        <br class="">
        <div class="">
          <blockquote type="cite" class="">
            <div class="">On 9 Nov 2017, at 15:44, Francesco Lamanna
              <<a href="mailto:francesco.lamanna@gmail.com" target="_blank" class="">francesco.lamanna@gmail.com</a>>
              wrote:</div>
            <br class="m_936139081383433000Apple-interchange-newline">
            <div class="">
              <div dir="ltr" class="">
                <div class="">
                  <div class="">
                    <div class="">
                      <div class="">
                        <div class="">Hi Mateus,<br class="">
                          <br class="">
                        </div>
                        thank you for your answer.<br class="">
                        <br class="">
                      </div>
                      I am using 'ncbi_db'   => 'mysql://<a href="http://anonymous@ensembldb.ensembl.org/ensembl_compara_90" target="_blank" class="">anonymous@ensembldb.<wbr class="">ensembl.org/ensembl_compara_90</a><wbr class="">'
                      to conncect to ncbi_db (I used the same value as
                      in the NoMasterProteinTrees_conf.pm example).<br class="">
                      <br class="">
                    </div>
                    The failing analysis is copy_ncbi_table(9).<br class="">
                    <br class="">
                  </div>
                  Cheers,<br class="">
                </div>
                Francesco.<br class="">
              </div>
              <div class="gmail_extra"><br class="">
                <div class="gmail_quote">2017-11-09 16:29 GMT+01:00
                  Mateus Patricio <span dir="ltr" class=""><<a href="mailto:mateus@ebi.ac.uk" target="_blank" class="">mateus@ebi.ac.uk</a>></span>:<br class="">
                  <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
                    <div style="word-wrap:break-word" class="">Hi
                      Francesco,
                      <div class=""><br class="">
                      </div>
                      <div class="">Looks like your pipeline is using
                        the user anonymous to connect to the database.</div>
                      <div class=""><br class="">
                      </div>
                      <div class="">I would suggest that you add the
                        skip option within your runnable.</div>
                      <div class=""><br class="">
                      </div>
                      <div class="">Which analysis is actually failing?</div>
                      <div class=""><br class="">
                      </div>
                      <div class="">Cheers,</div>
                      <div class=""><br class="">
                      </div>
                      <div class="">Mateus.</div>
                      <div class=""><br class="">
                      </div>
                      <div class=""><br class="">
                      </div>
                      <div class="">
                        <div class="">
                          <blockquote type="cite" class="">
                            <div class="">
                              <div class="m_936139081383433000h5">
                                <div class="">On 8 Nov 2017, at 17:36,
                                  Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank" class="">francesco.lamanna@gmail.com</a>>
                                  wrote:</div>
                                <br class="m_936139081383433000m_-3216016505973850452Apple-interchange-newline">
                              </div>
                            </div>
                            <div class="">
                              <div class="">
                                <div class="m_936139081383433000h5">
                                  <div dir="ltr" class="">
                                    <div class="">
                                      <div class="">
                                        <div class="">
                                          <div class="">Hello,<br class="">
                                            <br class="">
                                          </div>
                                          I am trying to apply the
                                          ProteinTrees pipeline to a set
                                          of Ensembl and non-Ensembl
                                          genomes. <br class="">
                                          <br class="">
                                          When running the pipeline
                                          without a master database (via
                                          <a href="http://beekeeper.pl/" target="_blank" class="">beekeeper.pl</a>)
                                          I get the following error:<br class="">
                                          <br class="">
                                          ensembl_compara_90
                                          ncbi_taxa_node  | sed
                                          "s/ENGINE=MyISAM/ENGINE=InnoDB<wbr class="">/" |  mysql
                                          -h127.0.0.1 -P3306 -uroot
                                          -p$EHIVE_TMP_PASSWORD_0
                                          hd_cc141_test_protein_trees_no<wbr class="">_master_90'
                                          resulted in an error code=2<br class="">
                                          stderr is: mysql: [Warning]
                                          Using a password on the
                                          command line interface can be
                                          insecure.<br class="">
                                          mysqldump: Got error: 1044:
                                          Access denied for user
                                          'anonymous'@'%' to database
                                          'ensembl_compara_90' when
                                          doing LOCK TABLES <br class="">
                                          <br class="">
                                          <br class="">
                                        </div>
                                        Is there a way to pass
                                        --skip-lock-tables to the
                                        pipeline (e.g. in the conf file)
                                        in order to be able to dump the
                                        database?<br class="">
                                        <br class="">
                                      </div>
                                      Thanks,<br class="">
                                    </div>
                                    Francesco.<br class="">
                                    <div class="">
                                      <div class="">
                                        <div class=""><br class="">
                                          <br class="">
                                        </div>
                                      </div>
                                    </div>
                                  </div>
                                </div>
                              </div>
                              ______________________________<wbr class="">_________________<br class="">
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                            </div>
                          </blockquote>
                        </div>
                        <br class="">
                      </div>
                    </div>
                    <br class="">
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            </div>
          </blockquote>
        </div>
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      <br class="">
      <fieldset class="m_936139081383433000mimeAttachmentHeader"></fieldset>
      <br class="">
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