[ensembl-dev] VEP BUG - corrupt storable string

[Duarte Molha]

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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