<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="">In your case the solution should be starting the LoadMembers without the option “<span style="font-family: 'Courier New';" class="">--collection ensembl</span>”.</div><div class=""><br class=""></div><div class="">If you start the pipeline without it, it should use all the current species in your master database.</div><div class=""><br class=""></div><div class="">In Ensembl we have different collections that are used for different purposes, and the default one is “<span style="font-family: 'Courier New';" class="">ensembl</span>”.</div><div class=""><br class=""></div><div class="">Please let me know if this works.</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><blockquote type="cite" class=""><div class="">On 11 Jan 2018, at 10:13, 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="">Hi Mateus,<br class=""><br class=""></div>many thanks for your answer.<br class=""><br class=""></div>I am trying to launch the LoadMembers pipeline in order to make a member_db, but I get the following error:<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="">| 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 |<br class="">| 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 |<br class="">| 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 |<br class="">| 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 |<br class="">| 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 |<br class="">| 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 |<br class="">+-------------+------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br class="">6<br class=""><br class=""></div>Cheers,<br class=""></div>Francesco. <br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2018-01-10 17:31 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=""><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=""><a href="http://init_pipeline.pl/" target="_blank" class="">init_pipeline.pl</a> Bio::EnsEMBL::Compara::<wbr class="">PipeConfig::EBI::Ensembl::<wbr class="">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 class="">mysql://ensro@host:port/<wbr class="">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 class=""><blockquote type="cite" class=""><div class=""><div class="h5"><div class="">On 10 Jan 2018, at 16:06, Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank" class="">francesco.lamanna@gmail.com</a>> wrote:</div><br class="m_-3026777456766023304Apple-interchange-newline"></div></div><div class=""><div class=""><div class="h5"><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="">+-------------+---------------<wbr class="">----------------+-------------<wbr class="">---+--------+---------+-------<wbr class="">----+---------------------+---<wbr class="">----+--------------+----------<wbr class="">------------------------------<wbr class="">------------------------------<wbr class="">--------------+----------+<br class="">| analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg <wbr class=""> <wbr class=""> | is_error |<br class="">+-------------+---------------<wbr class="">----------------+-------------<wbr class="">---+--------+---------+-------<wbr class="">----+---------------------+---<wbr class="">----+--------------+----------<wbr class="">------------------------------<wbr class="">------------------------------<wbr 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 <wbr class=""> | 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 <wbr class=""> | 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 <wbr class=""> | 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="">+-------------+---------------<wbr class="">----------------+-------------<wbr class="">---+--------+---------+-------<wbr class="">----+---------------------+---<wbr class="">----+--------------+----------<wbr class="">------------------------------<wbr class="">------------------------------<wbr 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></div></div>
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