[ensembl-dev] VEP: Exception thrown for rs28635379 PAR when using cache

[Oliver Burren]

Hi,

I was running VEP pretty successfully, until I got to PAR Y snp 
rs28635379 (http://bit.ly/z0r0wU)

Input like this (named test)

Y    59214011    59214011    A/C    +

Ran

perl variant_effect_predictor.pl -i test --cache --dir 
xxxx/ensembl_vep/data/ --sift=b --polyphen=b --condel=b --xref_refseq 
--regulatory -o test.out --force --verbose --debug

got

#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

version 2.4

By Will McLaren (wm2 at ebi.ac.uk)

Configuration options:

cache              1
condel             b
core_type          core
debug              1
dir                /xxxxx/ensembl_vep/data/
force_overwrite    1
host               ensembldb.ensembl.org
input_file         test
output_file        test.out
polyphen           b
port               5306
regulatory         1
sift               b
species            homo_sapiens
toplevel_dir       /xxxx/ensembl_vep/data/
verbose            1
xref_refseq        1


Bunch of progress stuff then an exception

-------------------- EXCEPTION --------------------
MSG: Sequence NNNNNNNNNNN contains invalid characters: Only Aa Cc Gg Tt accepted
STACK Bio::EnsEMBL::Funcgen::BindingMatrix::relative_affinity xxx/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/BindingMatrix.pm:296
STACK Bio::EnsEMBL::Variation::MotifFeatureVariationAllele::motif_score_delta xxx/ensembl-variation/modules/Bio/EnsEMBL/Variation/MotifFeatureVariationAllele.pm:169
STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_to_consequences xxxx/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm:1001
STACK Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences xxxx/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm:885
STACK main::main xxxx/ensembl_vep/variant_effect_predictor.pl:185
STACK toplevel xxxxx/ensembl_vep/variant_effect_predictor.pl:69
Ensembl API version = 66
---------------------------------------------------


If I do this

perl variant_effect_predictor.pl -i test  --sift=b --polyphen=b 
--condel=b --xref_refseq --regulatory -o test.out --force --verbose --debug

or use the online tool all is well

Same error if you use e65 software/cache.

Anyone got any ideas ?

Thanks,

Olly Burren