[ensembl-dev] ensembl compara : warning messages

[Matthieu Muffato]

Hi Benoît,

v73 of the Compara API is indeed more verbose about missing core 
databases. This exhaustive search is triggered when the API cannot not 
naturally find a species in the Registry (e.g "homo sapiens" instead of 
"homo_sapiens", etc).

We had a few cases in previous releases where the Compara API was not 
reporting missing links, hence the change in e73. I understand there are 
too many warnings, and this has been improved in e74. The change was 
unfortunately too big to backport to e73 after the public release, so 
I'd suggest you simply comment the line 444 out in GenomeDB.pm


Hope this helps,
Matthieu


On 12/12/13 17:04, Benoît Ballester wrote:
> Hi everyone,
>
> I am using the v73 API against databases (human + compara) installed on a local server.
> I do not have all core databases on the server, and I use a registry conf file with just human and compara in it.
>
> I get these warning messages (see below)
> Could you please advice on how to turn them off please ? I am sure I am missing something obvious.
>
> Thanks,
>
> Ben
>
>
> Cannot find the core database of 'pelodiscus_sinensis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
> Cannot find the core database of 'xiphophorus_maculatus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
> Cannot find the core database of 'mustela_putorius_furo' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
> Cannot find the core database of 'felis_catus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
> Cannot find the core database of 'rattus_norvegicus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
> Cannot find the core database of 'gallus_gallus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
> Cannot find the core database of 'caenorhabditis_elegans' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
> Cannot find the core database of 'anas_platyrhynchos' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
> Cannot find the core database of 'ficedula_albicollis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>