[ensembl-dev] Chimp alignment for Chromosome Y

[Yuan Chen]

Hi ALL,

I am using Ensembl Compara to pull out chimp sequences for corresponding human bases, most of them are correct, but for a few of them, I got  chimp bases that are different from human reference base, but UCSC has the same base as human reference base :

Ensembl API version is 63
genomedb_name is homo_sapiens
genomedb_name is pan_troglodytes
alignment_type is BLASTZ_NET
chimp_slices is 1
num slice is 1
name of the slice is pan_troglodytes
ref_base is G and ref_pos is 2691796 and chimp base is A and chimp_pos is 23773099 and 1
chimp_slices is 1
num slice is 1
name of the slice is pan_troglodytes
ref_base is G and ref_pos is 2750827 and chimp base is T and chimp_pos is 23713497 and 2
chimp_slices is 1
num slice is 1
name of the slice is pan_troglodytes
ref_base is A and ref_pos is 2836431 and chimp base is T and chimp_pos is 23626512 and 3
chimp_slices is 1
num slice is 1
.............. 


When I changed to run ensembl version 65, I got error message :

-------------------- WARNING ----------------------
MSG: No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for
 <BLASTZ_NET> and homo_sapiens(GRCh37), pan_troglodytes(CHIMP2.1.4)
FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 681
CALLED BY: svn/modules/AncestralBase.pm  LINE: 122
Ensembl API version = 65
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: [] is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
STACK Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::fetch_by_Slice_MethodLinkSpeciesSet /nfs/team19/yuan/ensembl-checkout/ensembl-compara-65/modules/Bio/EnsEMBL/Compara/DBSQL/AlignSliceAdaptor.pm:138
STACK AncestralBase::get_ancestral_allele_by_slices_from_db /nfs/users/nfs_y/yuan/sanger/src/svn/modules/AncestralBase.pm:135
STACK main::get_base_from_pos_file ./get_ancestral_allele.pl:111
STACK toplevel ./get_ancestral_allele.pl:51
Ensembl API version = 65
---------------------------------------------------
Ensembl API version is 65
genomedb_name is homo_sapiens
genomedb_name is pan_troglodytes
alignment_type is BLASTZ_NET

Any idea what went wrong please?

Thanks

yuan
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