<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">beekeper.pl</a> I get stuck at the load_genomedb stage with the following message:<br><br>mysql> SELECT * FROM msg;<br>+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<br>| analysis_id | logic_name                    | log_message_id | job_id | role_id | worker_id | when_logged         | retry | status       | msg                                                                                                                                                                                                                                                 | is_error |<br>+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<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                                                                                                                                                                                                   |        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                                                                                                                                                                                                   |        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                                                                                                                                                                                                           |        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/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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_floridae', assembly_name='V2' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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-5.0' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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_milii', assembly_name='6.1.3' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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_marinus', assembly_name='germline_final' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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-5.0' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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_marinus', assembly_name='germline_final' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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_floridae', assembly_name='V2' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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_milii', assembly_name='6.1.3' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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_floridae', assembly_name='V2' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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_milii', assembly_name='6.1.3' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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-5.0' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/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_marinus', assembly_name='germline_final' on the servers provided, please investigate at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/LoadOneGenomeDB.pm line 179. |        1 |<br>+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+<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>+--------------+----------+------------------------+-------------------+-----------------+---------------+------------------+------------------+-------------+--------------+---------+---------------+--------------+<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>+--------------+----------+------------------------+-------------------+-----------------+---------------+------------------+------------------+-------------+--------------+---------+---------------+--------------+<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>+--------------+----------+------------------------+-------------------+-----------------+---------------+------------------+------------------+-------------+--------------+---------+---------------+--------------+</div><div><br></div><div>I attach the pipeline and the registry conf files for completeness.</div><div><br></div><div>Thank you for your help,</div><div>Francesco.<br></div></div>