[ensembl-dev] Uncached variants + Offline mode

[William McLaren]

If you've only run in offline mode you should be fine, but if you want to make sure then perhaps do it for peace of mind!

Will



On 2 Oct 2015 14:46, Sebastian Ginzel <sginze2s at inf.h-brs.de> wrote:
>
> Hi Will,
>
> the --write-cache option was enabled, I don't remember why or who enabled it. I think I can safely remove it from my command line, but I guess I should re-download the cache?
>
> Regards,
> Sebastian Ginzel
>
> On 01.10.2015 17:07, Will McLaren wrote:
>>
>> Hi Sebastian,
>>
>> Can you share your full command line?
>>
>> That line of code should not be triggered unless you have either --database (which should cause the script to fail on startup) or --write_cache (which you shouldn't use unless you really know what you're doing!) enabled.
>>
>> Regards
>>
>> Will McLaren
>> Ensembl Variation
>>
>> On 1 October 2015 at 14:16, Sebastian Ginzel <sginze2s at inf.h-brs.de> wrote:
>>>
>>> Hi,
>>>
>>> I am using VEP 80 and use the --offline and --cache option, which usually works fine, but now fails on one input file with the message:
>>>
>>> Can't call method "db" on an undefined value at /path_to_lib/ensembl_80/lib/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 6360, <GEN0> line 190004
>>>
>>> After digging into the code I found that this line is called when a variant is not available in the cache and VEP tries to retrieve the information from the database via through the get_variations_from_region function.
>>>
>>> The line where the script fails is:
>>>     if(defined($config->{vfa}->db)) {
>>>
>>> Other functions such as 'have_pubmed' have an additional condition which prevents the error:
>>>     if(defined($config->{vfa}) && defined($config->{vfa}->db)) {
>>>
>>> I fixed the error for my VEP script by adding the "defined($config->{vfa})" condition. But now I am wondering if the error is intentional and if not which should be the default return value, if the script is running in offline mode.
>>>
>>>
>>> Best wishes,
>>> Sebastian Ginzel
>>>
>>>
>>>
>>>
>>>
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>>
>>
>>
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>