[ensembl-dev] Bad data in MySQL dumps

Nathan Johnson njohnson at ebi.ac.uk
Thu Apr 14 10:13:35 BST 2011


Hi Fedor.

Leaving the result_feature data out will mean you will not be able to  
display any wiggle tracks at all. So not so much a trade as an omission.

Nath


On 14 Apr 2011, at 09:52, Fedor Gusev wrote:

> Hmm... Does this mean I can safely leave this table empty, trading
> speed for that?
>
> On Mon, Apr 11, 2011 at 12:14 PM,  <njohnson at ebi.ac.uk> wrote:
>> Hi Fedor
>>
>> The error would seem to be correct, the rough footprint for this  
>> table for
>> v61 was 193GB. This is web optimised data, designed to speed up the  
>> wiggle
>> track displays.  For v62 this has been moved outside of the  
>> database for
>> various reasons, there will be a blog post about this shortly.
>>
>> wrt the gunzip -l output, that does seem a little odd. I will see  
>> if I can
>> recreate.
>>
>> Nath
>>
>>> Basically, it says:
>>>   gzip: result_feature.txt: No space left on device
>>> And i have >100Gb left on this partition.
>>>
>>> gunzip -l reports this:
>>>         compressed        uncompressed  ratio uncompressed_name
>>>         11304575360          1712567965 -560.1% result_feature.txt
>>> Seems kinda weird.
>>>
>>>
>>> On Fri, Apr 8, 2011 at 4:42 PM, Nathan Johnson  
>>> <njohnson at ebi.ac.uk> wrote:
>>>> Hi Fedor
>>>>
>>>> Can you be more specific when you say 'fails to unpack'? What  
>>>> happens
>>>> exactly?
>>>>
>>>> I suspect what you are seeing is that it is taking a long time to  
>>>> unpack
>>>> as these files are particularly large.  Also, please see the README
>>>> file for more information on how to handle the result_feature  
>>>> imports,
>>>> as they require some non-standard parameters to handle the BLOB  
>>>> data.
>>>>
>>>> Thanks
>>>>
>>>>
>>>> Nath
>>>>
>>>> On 3 Apr 2011, at 12:14, Fedor Gusev wrote:
>>>>
>>>>> Hello everyone.
>>>>>
>>>>> I have some problems with file
>>>>>  ftp://ftp.ensembl.org/pub/release-61/mysql/homo_sapiens_funcgen_61_37f/result_feature.txt.gz
>>>>>
>>>>> It is not present in CHECKSUMS file and fails to unpack. Can you
>>>>> please check on this?
>>>>>
>>>>> --
>>>>> Kind regards,
>>>>> Fedor Gusev.
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list
>>>>> Dev at ensembl.org
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>
>>>> Nathan Johnson
>>>> Senior Scientific Programmer
>>>> Ensembl Regulation
>>>> European Bioinformatics Institute
>>>> Wellcome Trust Genome Campus
>>>> Hinxton
>>>> Cambridge CB10 1SD
>>>>
>>>> http://www.ensembl.info/
>>>> http://twitter.com/#!/ensembl
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Kind regards,
>>> Fedor Gusev.
>>>
>>
>>
>>
>
>
>
> -- 
> Kind regards,
> Fedor Gusev.





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