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

[Will McLaren]

Hi Oliver,

The problem has now been fixed - you will need to re-download the
cache file from the FTP site.

Thanks for your patience

Will

On 29 February 2012 16:14, Oliver Burren <oliver.burren at cimr.cam.ac.uk> wrote:
> 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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>>
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>
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