<div dir="ltr"><div><div>Hi all,<br><br></div>I am trying to run the Compara 
protein-tree pipeline (v91) on a set of two core ensembl genomes and 
three custom genomes (stored locally) using a master database.<br><br></div>when I run <a href="http://beekeper.pl" target="_blank">beekeper.pl</a> I get stuck at the load_genomedb stage with the following message:<br><br>mysql> SELECT * FROM msg;<br>+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<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>                              <wbr>                              <wbr>                              <wbr>    | is_error |<br>+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-------------------------+----<wbr>------+<br>|          
 9 | copy_ncbi_table               |              1 |      5 |       3 
|         3 | 2017-12-12 17:56:51 |     0 | WRITE_OUTPUT | Successfully 
copied 1609518 'ncbi_taxa_node' rows                          <wbr>                              <wbr>                              <wbr>                              <wbr>                              <wbr>                              <wbr>                   |        0 |<br>|          
 9 | copy_ncbi_table               |              2 |      6 |       4 
|         4 | 2017-12-12 17:58:43 |     0 | WRITE_OUTPUT | Successfully 
copied 2438889 'ncbi_taxa_name' rows                          <wbr>                              <wbr>                              <wbr>                              <wbr>                              <wbr>                              <wbr>                   |        0 |<br>|         
 10 | populate_method_links_from_db |              3 |      7 |       6 
|         6 | 2017-12-12 18:00:20 |     0 | WRITE_OUTPUT | Successfully 
copied 18 'method_link' rows                          <wbr>                              <wbr>                              <wbr>                              <wbr>                              <wbr>                              <wbr>                           |        0 |<br>|         
 13 | load_genomedb                 |              4 |     11 |       9 
|         9 | 2017-12-12 18:03:25 |     0 | FETCH_INPUT  | Could not 
find species_name='homo_sapiens', assembly_name='GRCh38' on the servers 
provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.               |        1 |<br>|         
 13 | load_genomedb                 |              5 |     13 |      10 
|        10 | 2017-12-12 18:03:25 |     0 | FETCH_INPUT  | Could not 
find species_name='branchiostoma_<wbr>floridae', assembly_name='V2' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.         |        1 |<br>|         
 13 | load_genomedb                 |              6 |     12 |       9 
|         9 | 2017-12-12 18:03:26 |     0 | FETCH_INPUT  | Could not 
find species_name='gallus_gallus', assembly_name='Gallus_gallus-<wbr>5.0' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.   |        1 |<br>|         
 13 | load_genomedb                 |              7 |     15 |      10 
|        10 | 2017-12-12 18:03:26 |     0 | FETCH_INPUT  | Could not 
find species_name='callorhinchus_<wbr>milii', assembly_name='6.1.3' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.         |        1 |<br>|         
 13 | load_genomedb                 |              8 |     14 |      11 
|        12 | 2017-12-12 18:04:23 |     0 | FETCH_INPUT  | Could not 
find species_name='petromyzon_<wbr>marinus', assembly_name='germline_final' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179. |        1 |<br>|         
 13 | load_genomedb                 |              9 |     12 |      12 
|        11 | 2017-12-12 18:04:24 |     1 | FETCH_INPUT  | Could not 
find species_name='gallus_gallus', assembly_name='Gallus_gallus-<wbr>5.0' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.   |        1 |<br>|         
 13 | load_genomedb                 |             10 |     11 |      11 
|        12 | 2017-12-12 18:04:24 |     1 | FETCH_INPUT  | Could not 
find species_name='homo_sapiens', assembly_name='GRCh38' on the servers 
provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.               |        1 |<br>|         
 13 | load_genomedb                 |             11 |     14 |      12 
|        11 | 2017-12-12 18:04:25 |     1 | FETCH_INPUT  | Could not 
find species_name='petromyzon_<wbr>marinus', assembly_name='germline_final' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179. |        1 |<br>|         
 13 | load_genomedb                 |             12 |     13 |      13 
|        14 | 2017-12-12 18:05:25 |     1 | FETCH_INPUT  | Could not 
find species_name='branchiostoma_<wbr>floridae', assembly_name='V2' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.         |        1 |<br>|         
 13 | load_genomedb                 |             13 |     11 |      14 
|        13 | 2017-12-12 18:05:25 |     2 | FETCH_INPUT  | Could not 
find species_name='homo_sapiens', assembly_name='GRCh38' on the servers 
provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.               |        1 |<br>|         
 13 | load_genomedb                 |             14 |     15 |      13 
|        14 | 2017-12-12 18:05:26 |     1 | FETCH_INPUT  | Could not 
find species_name='callorhinchus_<wbr>milii', assembly_name='6.1.3' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.         |        1 |<br>|         
 13 | load_genomedb                 |             15 |     13 |      14 
|        13 | 2017-12-12 18:05:26 |     2 | FETCH_INPUT  | Could not 
find species_name='branchiostoma_<wbr>floridae', assembly_name='V2' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.         |        1 |<br>|         
 13 | load_genomedb                 |             16 |     15 |      16 
|        16 | 2017-12-12 18:06:25 |     2 | FETCH_INPUT  | Could not 
find species_name='callorhinchus_<wbr>milii', assembly_name='6.1.3' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.         |        1 |<br>|         
 13 | load_genomedb                 |             17 |     12 |      15 
|        15 | 2017-12-12 18:06:25 |     2 | FETCH_INPUT  | Could not 
find species_name='gallus_gallus', assembly_name='Gallus_gallus-<wbr>5.0' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179.   |        1 |<br>|         
 13 | load_genomedb                 |             18 |     14 |      16 
|        16 | 2017-12-12 18:06:26 |     2 | FETCH_INPUT  | Could not 
find species_name='petromyzon_<wbr>marinus', assembly_name='germline_final' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/<wbr>EnsEMBL/ensembl-compara/<wbr>modules/Bio/EnsEMBL/Compara/<wbr>RunnableDB/LoadOneGenomeDB.pm line 179. |        1 |<br>+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-------------------------+----<wbr>------+<br><div><br></div><div>the genome_db table in the master database looks like this:</div><div><br></div><div>mysql> SELECT * FROM genome_db;<br>+--------------+----------+---<wbr>---------------------+--------<wbr>-----------+-----------------+<wbr>---------------+--------------<wbr>----+------------------+------<wbr>-------+--------------+-------<wbr>--+---------------+-----------<wbr>---+<br>|
 genome_db_id | taxon_id | name                   | assembly          | 
genebuild       | has_karyotype | is_high_coverage | genome_component | 
strain_name | display_name | locator | first_release | last_release |<br>+--------------+----------+---<wbr>---------------------+--------<wbr>-----------+-----------------+<wbr>---------------+--------------<wbr>----+------------------+------<wbr>-------+--------------+-------<wbr>--+---------------+-----------<wbr>---+<br>|           
 1 |     9606 | homo_sapiens           | GRCh38            | 
2014-01-Ensembl |             1 |                1 | NULL             | 
NULL        | Human        | NULL    |          NULL |         NULL |<br>|           
 2 |     9031 | gallus_gallus          | Gallus_gallus-5.0 | 
2016-06-Ensembl |             1 |                1 | NULL             | 
NULL        | Chicken      | NULL    |          NULL |         NULL |<br>|           
 3 |     7739 | branchiostoma_floridae | V2                | 
100             |             0 |                1 | NULL             | 
NULL        | NULL         | NULL    |          NULL |         NULL |<br>|           
 4 |     7757 | petromyzon_marinus     | germline_final    | 
PMZ_v3.1        |             0 |                1 | NULL             | 
NULL        | NULL         | NULL    |          NULL |         NULL |<br>|           
 5 |     7868 | callorhinchus_milii    | 6.1.3             | 
100             |             0 |                1 | NULL             | 
NULL        | NULL         | NULL    |          NULL |         NULL |<br>+--------------+----------+---<wbr>---------------------+--------<wbr>-----------+-----------------+<wbr>---------------+--------------<wbr>----+------------------+------<wbr>-------+--------------+-------<wbr>--+---------------+-----------<wbr>---+</div><div><br></div><div>I link below the pipeline and the registry conf files for completeness:</div><div><br></div><div><a href="https://drive.google.com/open?id=1mRknH2KgY7DL8mhEK1qlvNOwehpPMUd0">https://drive.google.com/open?id=1mRknH2KgY7DL8mhEK1qlvNOwehpPMUd0</a></div><div><br></div><div><a href="https://drive.google.com/open?id=1oogxEiE2fPfAJTkkHVs5Bb4bIvfLytFW">https://drive.google.com/open?id=1oogxEiE2fPfAJTkkHVs5Bb4bIvfLytFW</a><br></div><div><br></div><div>Thank you for your help,</div>Francesco.</div>