[ensembl-dev] VEP error

[Will McLaren]

Hi Matteo,

Strange - the subroutine containing that code should only be triggered with
the --debug flag active.

Perhaps you have a vep.ini file present with the debug flag active? I can't
see any other way it is being triggered.

In any case, the warning is harmless!

Regards

Will

On 23 May 2016 at 13:29, Matteo <matteodeg at gmail.com> wrote:

> Hi Will,
>
> I don't use --debug option in my command line, I only use these flags:
>
>     --cache \
>     --assembly GRCh37 \
>     --offline \
>     --force_overwrite \
>     -v \
>     --variant_class \
>     --sift b \
>     --poly b \
>     --vcf_info_field ANN \
>     --hgvs \
>     --protein \
>     --canonical \
>     --check_existing \
>     --gmaf \
>     --pubmed \
>     --species homo_sapiens \
>     --failed 1 \
>     --plugin LoFtool \
>     --vcf
>
> Thank you,
>
> matteo
>
>
> Il 23/05/2016 13:58, Will McLaren ha scritto:
>
> Hi Matteo,
>
> Remove the --debug flag from your command line; this is intended for use
> only by VEP developers.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 23 May 2016 at 12:35, Matteo <matteodeg at gmail.com> wrote:
>
>> Hi all,
>> I'm using the last VEP version (84).
>> I get this error:
>>
>> Negative repeat count does nothing at
>> ~/NGS_TOOLS/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 6906.
>> [>                                              ]    [ 0% ]Negative
>> repeat count does nothing at
>> /home/jarvis/NGS_TOOLS/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 6906.
>> [>                                              ]    [ 0% ]Negative
>> repeat count does nothing at
>> /home/jarvis/NGS_TOOLS/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
>> line 6906.
>> [===============================================]  [ 100% ]
>>
>> However, the annotation seems to be ok. Any idea?
>> Thanks,
>>
>> Matteo
>>
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>
>
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