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

[Will McLaren]

Hi Oliver,

My apologies, there seems to be a particular issue with the caching of
regulatory feature sequences on chromosome Y.

I'm investigating this and should have a fix sometime soon, but in the
meantime you can use the VEP without the cache and it should work.

Cheers

Will McLaren
Ensembl Variation

On 29 February 2012 12:51, Oliver Burren <oliver.burren at cimr.cam.ac.uk> wrote:
> 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
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/