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

[namchul ghim]

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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