<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>