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

[Oliver Burren]

Hi Will,

OK so I have downloaded this, I wrote a script to 'md5' the other cache 
files to see if they had changed and it looks as though they have.

e.g. (Where 'data' is original and 'data2' is the latest).
5d8ad754aa45bbfacf6141f058a569a1 
ensembl_vep/data2/homo_sapiens/66/11/34000001-35000000_reg.gz
4ee044abe0a9a5f8b608bb1e4c4f7a68  
ensembl_vep/data/homo_sapiens/66/11/34000001-35000000_reg.gz

Do I need to rerun my whole analysis (for all chromosomes) or can I 
ignore these differences and just run on the Y ?

Thanks,

O

On 02/03/12 11:30, Will McLaren wrote:
> 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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