[ensembl-dev] VEP BUG - corrupt storable string

Will McLaren wm2 at ebi.ac.uk
Fri Sep 14 10:03:53 BST 2012


Hi Duarte,

I've committed a fix to the CVS tree for this, hopefully this will
prevent the problems you were having.

Thanks

Will

On 10 September 2012 18:04, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:
> Thank you...
> Sorry for insisting, but because you had asked me for more details about the bug I wanted to make sure I had provided you will all the information you required. I did not mean to rush you guys :-)
>
> Cheers
>
> Duarte
>
> -----Original Message-----
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
> Sent: 10 September 2012 16:20
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] VEP BUG - corrupt storable string
>
> Hi Duarte,
>
> We are looking into this - rest assured we'll get back to you if we track down the cause of the errors.
>
> Will
>
> On 10 September 2012 15:52, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:
>> Any news regarding these bugs?
>>
>> Cheers
>>
>> Duarte
>>
>> -----Original Message-----
>> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On
>> Behalf Of Duarte Molha
>> Sent: 06 September 2012 10:48
>> To: Ensembl developers list
>> Subject: Re: [ensembl-dev] VEP BUG - corrupt storable string
>>
>> My apologies Will, I know should have done it... but now the script is not giving me this error anymore so I would not be surprised if it was user error (me) in this case.
>>
>> In attachment is a config file I am using to annotate a large VCF file
>>
>> The two only recurrent bugs I am still getting have to do with the
>> fork parameter and with memory not getting released from the script
>>
>> 1) when running with no forks, the script runs fine but it appears that memory does not get deallocated from the script so all RAM and cache gets used and eventually the script dies.
>> 2) when using the fork parameter, the script eventually crashes, but I
>> do not believe it to be related to filling the RAM like the previous
>> case. The script just crashes and outputs a bunch of garbled text
>>
>> I hope this is more usefull than my previous bug report.
>>
>> Best regards
>>
>> Duarte
>>
>> -----Original Message-----
>> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On
>> Behalf Of Will McLaren
>> Sent: 06 September 2012 09:51
>> To: Ensembl developers list
>> Subject: Re: [ensembl-dev] VEP BUG - corrupt storable string
>>
>> Hi Duarte,
>>
>> For this, and any future bug reports, it would be really helpful if you could relay the conditions that give rise to this error i.e. the input, options used etc.
>>
>> Thanks
>>
>> Will
>>
>> On 4 September 2012 15:59, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:
>>> I would like to report another VEP bug that has been killing my script:
>>>
>>>
>>>
>>> Corrupted storable string (binary v2.7) at ../../lib/Storable.pm
>>> (autosplit into ../../lib/auto/Storable/thaw.al) line 415, <CHILD>
>>> line 301427, at
>>> /NGS_Tools/bin/VEP_26_testing/Bio/EnsEMBL/Variation/Utils/VEP.pm line
>>> 970
>>>
>>>
>>>
>>>
>>>
>>> Duarte Molha
>>>
>>>
>>>
>>>
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>>
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