<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi Francesco</div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">This members database can be created by running the LoadMembers pipeline.</div><div class=""><br class=""></div><div class="">You can initiate the pipeline with the following command line:</div><div class=""><br class=""></div><div class=""><font face="Courier New" class="">init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::EBI::Ensembl::LoadMembers_conf --collection ensembl</font></div><div class=""><br class=""></div><div class="">Then you should point the parameter reuse_db to this database on your Protein Tree config file.</div><div class=""><br class=""></div><div class=""><font face="Courier New" class="">'reuse_db' => '<a href="mysql://ensro@host:port/database" class="">mysql://ensro@host:port/database</a>',</font></div><div class=""><br class=""></div><div class="">Please do let me know if you have further questions.</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><blockquote type="cite" class=""><div class="">On 10 Jan 2018, at 16:06, 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 all,<br class=""><br class=""></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 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 | 4 | 2018-01-10 16:40:13 | 0 | WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows | 0 |<br class="">| 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 |<br class="">| 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 |<br class="">| 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 class="">| 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 class="">+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------------------------------+----------+<br class=""><br class=""></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 class=""><br class=""></div>Can anyone please help me to solve this issue?<br class=""><br class=""></div>Thanks,<br class=""></div>Francesco.<br class=""></div>
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