[ensembl-dev] vep warning when using cache

[Nicolas Thierry-Mieg]

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.