[ensembl-dev] vep warning when using cache

[Guillermo Marco Puche]

Hello,

After a few weeks off and re-testing all the possible workarounds I can 
conclude that "indexing" VEP cache with convert_cache.pl script brakes it.
I've now two versions of VEP 80 cache, 1) out of the box (non indexed) 
2) indexed with convert_cache.pl
When I use 1) I get all the warnings, when I use version 2) performance 
is much better but I get tons and tons of warnings like those posted in 
previous mails.

I've tried indexing with tabix 0.2.5 and 0.2.6 and I get same warnings. 
So I don't think tabix version is the problem.
I hadn't this issue when I was using convert_cache.pl from version 75 
build. Any ideas what could have changed in this script to cause this 
behavior? Indexing cache with convert_cache.pl finishes correctly 
without any warning or error.

Regards,
Guillermo.


On 12/06/15 15:43, 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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