[ensembl-dev] vep warning when using cache

Tue Jul 7 12:54:36 BST 2015

Sorry I misswrote, when using 1) I get no warnings, when I use cache 2) 
I get the warnings.

On 07/07/15 13:53, Guillermo Marco Puche wrote:
> 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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>
>

-- 
Guillermo Marco Puche - Firma
------------------------------------------------------------------------

*Guillermo Marco Puche*

Bioinformatician, Computer Science Engineer
Sistemas Genómicos S.L.
Phone: +34 902 364 669 (Ext.777)
Fax: +34 902 364 670
www.sistemasgenomicos.com

<https://www.sistemasgenomicos.com/web_sg/web/areas-bioinformatica.php>

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