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

[Will McLaren]

Hi Oliver,

You should be OK to just rerun Y.

There will be a different MD5 as there is a tiny change in one of the
data structures stored in all of the cached files; this change only
has the effect of fixing the bug you encountered, it does not change
the data itself.

Cheers

Will

On 7 March 2012 11:13, Oliver Burren <oliver.burren at cimr.cam.ac.uk> wrote:
> 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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