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

[Oliver Burren]

Hi Will,

Thanks for the speedy reply. I'll do as you suggest.

O

On 29/02/12 15:52, Will McLaren wrote:
> 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
>>
>>
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