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

[Nick Langridge]

Ok will do, please let me know when ready.

Cheers,
Nick

On 12/04/2012 16:10, Dan Staines wrote:
> 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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>