<div dir="ltr"><div><div><div><div>Hi Mateus,<br><br></div>if I try to initialize the LoadMemebers pipeline without “<span style="font-family:"Courier New"">--collection ensembl</span>”, I get the following error:<br><br>The following options are missing:<br> {'collection'}<br><br></div>I also tried to set 'collection' => undef, in the conf file, but I get another error:<br><br>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.<br><br></div>Cheers,<br></div>Francesco<br></div><div class="gmail_extra"><br><div class="gmail_quote">2018-01-11 12:01 GMT+01:00 Mateus Patricio <span dir="ltr"><<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@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 style="word-wrap:break-word">Hi Francesco,<div><br></div><div>In your case the solution should be starting the LoadMembers without the option “<span style="font-family:'Courier New'">--collection ensembl</span>”.</div><div><br></div><div>If you start the pipeline without it, it should use all the current species in your master database.</div><div><br></div><div>In Ensembl we have different collections that are used for different purposes, and the default one is “<span style="font-family:'Courier New'">ensembl</span>”.</div><div><br></div><div>Please let me know if this works.</div><div><br></div><div>Cheers,</div><div><br></div><div>Mateus.</div><div><div class="h5"><div><br></div><div><br><div><blockquote type="cite"><div>On 11 Jan 2018, at 10:13, Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a>> wrote:</div><br class="m_6553179308464348895Apple-interchange-newline"><div><div dir="ltr"><div><div><div><div>Hi Mateus,<br><br></div>many thanks for your answer.<br><br></div>I am trying to launch the LoadMembers pipeline in order to 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 | job_id | role_id | worker_id | when_logged | retry | status | msg <wbr> <wbr> <wbr> <wbr> <wbr> | 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 | WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows <wbr> <wbr> <wbr> <wbr> | 0 |<br>| 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 <wbr> <wbr> <wbr> <wbr> | 0 |<br>| 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/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/GenomeDBFactory.pm line 106. | 1 |<br>| 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/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/GenomeDBFactory.pm line 106. | 1 |<br>| 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/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/GenomeDBFactory.pm line 106. | 1 |<br>| 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/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/GenomeDBFactory.pm line 106. | 1 |<br>+-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-+----------+<br>6<br><br></div>Cheers,<br></div>Francesco. <br></div><div class="gmail_extra"><br><div class="gmail_quote">2018-01-10 17:31 GMT+01:00 Mateus Patricio <span dir="ltr"><<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@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 style="word-wrap:break-word"><div>Hi Francesco</div><div><br></div><div>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.</div><div><br></div><div>This members database can be created by running the LoadMembers pipeline.</div><div><br></div><div>You can initiate the pipeline with the following command line:</div><div><br></div><div><font face="Courier New"><a href="http://init_pipeline.pl/" target="_blank">init_pipeline.pl</a> Bio::EnsEMBL::Compara::PipeCon<wbr>fig::EBI::Ensembl::LoadMembers<wbr>_conf --collection ensembl</font></div><div><br></div><div>Then you should point the parameter reuse_db to this database on your Protein Tree config file.</div><div><br></div><div><font face="Courier New">'reuse_db' => '<a>mysql://ensro@host:port/datab<wbr>ase</a>',</font></div><div><br></div><div>Please do let me know if you have further questions.</div><div><br></div><div>Cheers,</div><div><br></div><div>Mateus.</div><div><br></div><div><br></div><div><blockquote type="cite"><div><div class="m_6553179308464348895h5"><div>On 10 Jan 2018, at 16:06, Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a>> wrote:</div><br class="m_6553179308464348895m_-3026777456766023304Apple-interchange-newline"></div></div><div><div><div class="m_6553179308464348895h5"><div dir="ltr"><div><div><div><div><div>Hi all,<br><br></div>when I try to run the protein tree pipeline (v91) using the core Human and Chicken genomes I get the following error message:<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> <wbr> | is_error |<br>+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br>| 9 | copy_ncbi_table | 1 | 5 | 3 | 4 | 2018-01-10 16:40:13 | 0 | WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows <wbr> | 0 |<br>| 9 | copy_ncbi_table | 2 | 6 | 4 | 3 | 2018-01-10 16:42:04 | 0 | WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name' rows <wbr> | 0 |<br>| 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 <wbr> | 0 |<br>| 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 |<br>| 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 |<br>+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br><br></div>I have no clue about what to put in the 'reuse_db' parameter (nor could I find any information in the compara docs). <br><br></div>Can anyone please help me to solve this issue?<br><br></div>Thanks,<br></div>Francesco.<br></div></div></div>
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