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

[Oliver Burren]

Great - I was hoping you would say that !

Thanks for your help.

O

On 07/03/12 11:25, Will McLaren wrote:
> 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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