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

[Dan Staines]

There are a number of problems with the v66 version of the compara db 
for bacteria, so I'd advise testing using a new build that I'm about to 
finish to see if these problems persist.

On 04/12/2012 04:06 PM, 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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-- 
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/