[Gmod-help] Re: [Gmod-gbrowse] Database crash when loading genotypes

[Kate McGee]

Actually I ran the mySQL "isamchk -r" command and it repaired the  
table.  There was an issue with the indexing.

The problem is that every time I load a large amount of genotype data  
(I have been doing it one chromosome at a time), it corrupts the table  
again.  So I am going to finish loading it, run isamchk and see if it  
can repair the table again with even more data in it.

Kate


On Feb 12, 2009, at 12:51 PM, Dave Clements, GMOD Help Desk wrote:

> Kate,
>
> Were you ever successful at loading the data?  My usual problem with
> large datasets is running out of space on one of my disks.
>
> If not, can you post the specific error you are getting?
>
> Thanks,
>
> Dave C.
>
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>
>
> On Fri, Jan 30, 2009 at 6:21 AM, Erick Antezana <erant at psb.vib-ugent.be 
> > wrote:
>> A colleague just told me, he was able to load the hapmap stuff in  
>> GBrowse
>> 1.69 too.
>>
>> Erick
>>
>>> Hi,
>>>
>>> I have a very large amount of genotype data (~2000 individuals,
>>> 700,000 SNPs) that I would like to load into our mysql database so
>>> that it can be downloaded from our browser.  After loading three
>>> chromosomes our mysql database crashed.  It is being loaded into the
>>> fattribute_to_feature table in a text field.  Has anyone had success
>>> storing/loading this much data?
>>>
>>> Thanks,
>>> Kate
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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--------------------------------
Kate McGee, Ph.D.
Postdoctoral Fellow
National Cancer Institute at Frederick
Office: Building 559, Room 5
Phone: (301) 846-5425
mcgeekm at mail.nih.gov