[ensembl-dev] vep warning when using cache

[Hiram Clawson]

Try using LANG=C everywhere

You can force this on the entire system by setting the file /etc/default/locale to:
LANG="C"

then 'locale' will have "C" for all LC settings.  The 'sort' command is
a mess if it isn't always working in "C"

--Hiram

On 6/12/15 6:43 AM, Guillermo Marco Puche wrote:
> Hi Nicolas,
>
> Locale is exactly the same on both machines.
>
> LANG=en_US.UTF-8
> LANGUAGE=en_US
> LC_CTYPE="en_US.UTF-8"
> LC_NUMERIC=es_ES.UTF-8
> LC_TIME=es_ES.UTF-8
> LC_COLLATE="en_US.UTF-8"
> LC_MONETARY=es_ES.UTF-8
> LC_MESSAGES="en_US.UTF-8"
> LC_PAPER=es_ES.UTF-8
> LC_NAME=es_ES.UTF-8
> LC_ADDRESS=es_ES.UTF-8
> LC_TELEPHONE=es_ES.UTF-8
> LC_MEASUREMENT=es_ES.UTF-8
> LC_IDENTIFICATION=es_ES.UTF-8
> LC_ALL=
>
> Tried export LC_ALL=C and I still got warnings on machine2. Anyways, thank you for your help.
>
> Regards,
> Guillermo.
>
> On 12/06/15 15:36, Nicolas Thierry-Mieg wrote:
>> On 06/12/2015 03:21 PM, Guillermo Marco Puche wrote:
>>> Hi Will,
>>>
>>> This is the command:
>>>
>>>   * variant_effect_predictor.pl -i example_GRCh38.vcf -o
>>>     annotation_example_GRCh38.vcf -database -hgvs -cache -dir_cache
>>>     /home/gmarco/ensembl_80/cache
>>>
>>> I've tried on another machine (machine2) and I dont' get the error.
>>> Gonna try to re-install the exact same version of Perl on both machines.
>>> If this continues failing then I've no idea what's going on.
>>> Tried both version of bioperl 1.2.3 and 1.6.1 on both machines and both
>>> work good on machine2 and show warnings on machine1.
>>> Tried both versions of tabix 0.2.5 and 0.2.6 on both machines and both
>>> work good on machine2 and show warnings on machine1.
>>>
>>>   * Machine1 Warnings:
>>>     This is perl 5, version 14, subversion 4 (v5.14.4) built for
>>>     x86_64-linux
>>>
>>>   * Machine2 NO warnings:
>>>     This is perl 5, version 18, subversion 2 (v5.18.2) built for
>>>     x86_64-linux-gnu-thread-multi (with 41 registered patches, see perl
>>>     -V for more detail)
>>>
>>> Maybe it's not a perl issue. Then I've no clue what could be causing the
>>> issue.
>>
>> what does "locale" say on the two machines? I've had strange bugs before that were caused by
>> locale settings, as for example GNU "sort" behaves differently depending on that!
>> No idea if this could come into play with VEP, but try export LC_ALL=C before running the
>> command.
>>
>>
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>
>
>
>
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