[ensembl-dev] No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for...

[Javier Herrero]

Hi Nick

It seems like the server cannot find the information from the compara 
DB. Are you sure you have configured the compara DB correctly? If you 
have made any recent change to the server configuration, make sure you 
have deleted the packed files to force a reload of the configuration.

If the configuration is correct, check your compara database manually. 
Does it have an entry for BLASTZ_CHAIN in the method_link table? Is 
there anything there? It might be that your compara DB is broken.

Javier

On 12/04/12 16:06, Nick Langridge wrote:
> Hi,
>
> Multi-species view in EG Bacteria is broken at the moment - in the 
> logs I'm seeing a number of warnings relating to MethodLinkSpeciesSet.
> I'm not really sure what this is telling me, or where to start looking 
> for the source of the problem.
> Can anyone help me to understand these?
>
> Cheers
> Nick
>
> -------------------- WARNING ----------------------
> MSG: No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for
> <BLASTZ_NET> and e_coli_k12(EB1_e_coli_k12), e_coli_042(EB1_e_coli_042)
> FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 654
> CALLED BY: Compara/DBSQL/DnaAlignFeatureAdaptor.pm  LINE: 211
> Ensembl API version = 66
> ---------------------------------------------------
>
> -------------------- WARNING ----------------------
> MSG: No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for
> <LASTZ_NET> and e_coli_k12(EB1_e_coli_k12), e_coli_042(EB1_e_coli_042)
> FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 654
> CALLED BY: Compara/DBSQL/DnaAlignFeatureAdaptor.pm  LINE: 211
> Ensembl API version = 66
> ---------------------------------------------------
>
> -------------------- WARNING ----------------------
> MSG: No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for
> <TRANSLATED_BLAT> and e_coli_k12(EB1_e_coli_k12), 
> e_coli_042(EB1_e_coli_042)
> FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 654
> CALLED BY: Compara/DBSQL/DnaAlignFeatureAdaptor.pm  LINE: 211
> Ensembl API version = 66
> ---------------------------------------------------
>
> -------------------- WARNING ----------------------
> MSG: Meta table key 'max_align_2964' not defined and
> old meta table key 'max_alignment_length' not defined
>  -> using default value [20000]
> FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 797
> CALLED BY: EnsEMBL/Compara/MethodLinkSpeciesSet.pm  LINE: 522
> Ensembl API version = 66
> ---------------------------------------------------
>
> -------------------- WARNING ----------------------
> MSG: No method_link matches <BLASTZ_RAW>
> FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 914
> CALLED BY: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm  LINE: 647
> Ensembl API version = 66
> ---------------------------------------------------
>
> -------------------- WARNING ----------------------
> MSG: No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for
> <BLASTZ_RAW> and e_coli_k12(EB1_e_coli_k12), e_coli_042(EB1_e_coli_042)
> FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 654
> CALLED BY: Compara/DBSQL/DnaAlignFeatureAdaptor.pm  LINE: 211
> Ensembl API version = 66
> ---------------------------------------------------
>
> -------------------- WARNING ----------------------
> MSG: No method_link matches <BLASTZ_CHAIN>
> FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 914
> CALLED BY: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm  LINE: 647
> Ensembl API version = 66
> ---------------------------------------------------
>
> -------------------- WARNING ----------------------
> MSG: No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for
> <BLASTZ_CHAIN> and e_coli_k12(EB1_e_coli_k12), e_coli_042(EB1_e_coli_042)
> FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 654
> CALLED BY: Compara/DBSQL/DnaAlignFeatureAdaptor.pm  LINE: 211
> Ensembl API version = 66
> ---------------------------------------------------
>
>
>
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-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK