[ensembl-dev] vep warning when using cache

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Fri Jun 12 14:43:33 BST 2015


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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