[ensembl-dev] Is it a bug in ensembl_v79?

[namchul ghim]

OK,  thank you !




On Fri, Mar 20, 2015 at 6:19 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi again,
>
> We've patched in a fix for this that should prevent the script from
> exiting when encountering this scenario; again if you re-run INSTALL.pl and
> re-install the API you should get the fix.
>
> There is still an outstanding problem here, as the consequence type field
> for the particular variant type that causes this issue will be left blank.
>
> We're working on a complete fix for this that should be ready in the
> coming days.
>
> Will
>
> On 20 March 2015 at 08:55, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
>> Hello again,
>>
>> VEP.pm does not contain the impact() function itself, but it does refer
>> to objects on which that method may be called (if you're interested you'll
>> find the method in OverlapConsequence.pm).
>>
>> If you're still seeing the same error as above, it would be useful to
>> help us debug the problem if you could provide a line or two of input from
>> your VCF (or other input file) that recreates the error message.
>>
>> Thanks for the feedback
>>
>> Will McLaren
>> Ensembl Variation
>>
>> On 19 March 2015 at 23:21, namchul ghim <chulghim at gmail.com> wrote:
>>
>>> Thank you for your reponse.
>>>
>>> I ran INSTALL.PL again twice.
>>>
>>> but, VEP.pm doesn't contain impact() function still.
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Mar 18, 2015 at 6:27 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>>
>>>> Hello,
>>>>
>>>> The error you report is a bug that was fixed a couple of days ago; if
>>>> you update your API code (either re-run INSTALL.pl or use "git pull" in the
>>>> ensembl-variation directory if you installed the API from GitHub) you
>>>> should no longer see this error.
>>>>
>>>> The warning messages you see are because your input chromosome
>>>> coordinates are not valid for build GRCh38; note the difference in
>>>> chromosome length for chr22 between GRCh38:
>>>>
>>>> http://www.ensembl.org/Homo_sapiens/Location/Chromosome?r=22
>>>>
>>>> and GRCh37
>>>>
>>>> http://grch37.ensembl.org/Homo_sapiens/Location/Chromosome?r=22
>>>>
>>>> You should only use input files that have been called against or
>>>> remapped to GRCh38 when using the GRCh38 cache; the VEP does NOT do any
>>>> remapping for you. If you wish to remap your data from GRCh37 to GRCh38,
>>>> you can try the Assembly Converter tool - it comes as part of the
>>>> ensembl-tools package, or you can use it online here:
>>>> http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core
>>>>
>>>> Regards
>>>>
>>>> Will McLaren
>>>> Ensembl Variation
>>>>
>>>> On 18 March 2015 at 07:32, namchul ghim <chulghim at gmail.com> wrote:
>>>>
>>>>> After installing Ensembl_v79, I annotated vep cache with GRch37.
>>>>> When doing so I got a following message:
>>>>> Can't call method "impact" on an undefined value at
>>>>> /mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor
>>>>> /Bio/EnsEMBL/Variation/Utils/VEP.pm line 2379.
>>>>>
>>>>> When I checked the following source file, there is no definition of
>>>>> imapct() function. There is only function name in the same line.
>>>>> Isn't that a bug?
>>>>>
>>>>> Also, in same condition, annotating only vep cache with GRCh38 version
>>>>> was successful.
>>>>>
>>>>> What is going on?
>>>>>
>>>>> Additionally, when I was annotating vep cache with GRCh38 version,
>>>>> there is a warning message in cache file.
>>>>> The warning message is as follow:
>>>>> WARNING: Could not find variation cache for 22:51000001-52000000
>>>>> WARNING: Could not find variation cache for 22:51000001-52000000
>>>>> WARNING: Could not find variation cache for 22:51000001-52000000
>>>>> WARNING: Could not find variation cache for 22:51000001-52000000
>>>>> WARNING: Could not find cache for 22:51000001-52000000
>>>>> WARNING: Could not find cache for 22:51000001-52000000
>>>>>
>>>>> When I checked the actual cache folder, there is no file in such
>>>>> range. Is this something I should consider or can I ignore this message?
>>>>>
>>>>> For your information, the vep cahce is downloaded in this location:
>>>>>
>>>>> ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_vep_79_GRCh38.tar.gz
>>>>>
>>>>> Thank you very much!
>>>>>
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>>>>>
>>>>
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>>
>
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