[ensembl-dev] Problem with load_genomedb in the compara protein tree pipeline
Francesco Lamanna
francesco.lamanna at gmail.com
Tue Dec 12 17:50:39 GMT 2017
Hi all,
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.
when I run beekeper.pl I get stuck at the load_genomedb stage with the
following message:
mysql> SELECT * FROM msg;
+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
| analysis_id | logic_name | log_message_id | job_id |
role_id | worker_id | when_logged | retry | status |
msg
| is_error |
+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
the genome_db table in the master database looks like this:
mysql> SELECT * FROM genome_db;
+--------------+----------+------------------------+-------------------+-----------------+---------------+------------------+------------------+-------------+--------------+---------+---------------+--------------+
| genome_db_id | taxon_id | name | assembly |
genebuild | has_karyotype | is_high_coverage | genome_component |
strain_name | display_name | locator | first_release | last_release |
+--------------+----------+------------------------+-------------------+-----------------+---------------+------------------+------------------+-------------+--------------+---------+---------------+--------------+
| 1 | 9606 | homo_sapiens | GRCh38 |
2014-01-Ensembl | 1 | 1 | NULL |
NULL | Human | NULL | NULL | NULL |
| 2 | 9031 | gallus_gallus | Gallus_gallus-5.0 |
2016-06-Ensembl | 1 | 1 | NULL |
NULL | Chicken | NULL | NULL | NULL |
| 3 | 7739 | branchiostoma_floridae | V2 |
100 | 0 | 1 | NULL |
NULL | NULL | NULL | NULL | NULL |
| 4 | 7757 | petromyzon_marinus | germline_final |
PMZ_v3.1 | 0 | 1 | NULL |
NULL | NULL | NULL | NULL | NULL |
| 5 | 7868 | callorhinchus_milii | 6.1.3 |
100 | 0 | 1 | NULL |
NULL | NULL | NULL | NULL | NULL |
+--------------+----------+------------------------+-------------------+-----------------+---------------+------------------+------------------+-------------+--------------+---------+---------------+--------------+
I attach the pipeline and the registry conf files for completeness.
Thank you for your help,
Francesco.
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