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

[Will McLaren]

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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>
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