[ensembl-dev] Problem with load_genomedb in compara

[Francesco Lamanna]

Hi Mateus,

thank you for the answer.

I tried to implement your solution, but I get this type of error:

|          13 | load_genomedb                 |              4 |     13
|      10 |         9 | 2017-12-18 17:06:40 |     0 | FETCH_INPUT  | Sorry,
could not figure out how to make a DBConnection object out of
'Bio::EnsEMBL::Compara::GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_ensembl_species.jsonindex=1'
at
/beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Utils.pm
line 366.

thanks,
Francesco

2017-12-18 12:28 GMT+01:00 Mateus Patricio <mateus at ebi.ac.uk>:

> Hi Francesco,
>
> Could you please try adding the following to the locator field in
> the genome_db table for each of your custom genomes?
>
> Bio::EnsEMBL::Compara::GenomeMF/filename=/home/hd/hd_
> hd/hd_cc141/Vertebrates_project/Ensembl_compara/non_
> ensembl_species.jsonindex=1
>
>
> Please match the index=1, index=2 to the order in which each genomes are
> declared in your file.
>
> If your json file looks like this:
>
> {
>     "production_name" : "species1",
>     "taxonomy_id"     : "8508",
>     "cds_fasta"       : “species1.cds.fa",
>     "prot_fasta"      : "species1.prot.fa",
>     "gene_coord_gff"  : "species1.gff",
>     "source"          : "augustus_maker",
> },
>
> {
>     "production_name" : "species2",
>     "taxonomy_id"     : "8496",
>     "cds_fasta"       : “species2.cds.fa",
>     "prot_fasta"      : “species2.prot.fa",
>     "gene_coord_gff"  : "species2.gff",
>     "source"          : "refseq",
> },
>
> You could add this info to the genome_db table:
>
> INSERT INTO genome_db (locator) VALUES ('Bio::EnsEMBL::Compara::
> GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_
> project/Ensembl_compara/non_ensembl_species.jsonindex=1’) WHERE name =
> ’species1'
> INSERT INTO genome_db (locator) VALUES ('Bio::EnsEMBL::Compara::
> GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_
> project/Ensembl_compara/non_ensembl_species.jsonindex=2’) WHERE name =
> ’species2’
>
> I hope that helps.
>
> Cheers,
>
> Mateus.
>
>
> On 14 Dec 2017, at 17:17, Francesco Lamanna <francesco.lamanna at gmail.com>
> wrote:
>
> 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 beekeeper.pl script load_genomedb fails to find my local
> genomes (but it loads correctly the ensembl core genomes), and drops this
> kind of error message:
>
> 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.
>
> the information regarding the local genomes is stored in a .json file and
> loaded in the genome_db table of the master database. The .json file is
> invoked in pipeline conf script using:
>
> 'curr_file_sources_locs'  => [ '/home/hd/hd_hd/hd_cc141/
> Vertebrates_project/Ensembl_compara/non_ensembl_species.json' ]
>
> Thank you for your help,
> Francesco.
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