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

[Kate McGee]

Database corruption doesn't make me feel warm and fuzzy either!

1) I haven't heard from anyone saying they were having this problem  
and didn't come across anything when I searched the mailing list  
archives
2) We are running mySQL version 5.0.27 and I just updated GBrowse, so  
I think this would update the bp_load_gff.pl script?

I haven't tried loading since I updated GBrowse.  I wonder if this  
would make a difference or if this is purely a mySQL issue?

Thanks
Kate


On Feb 12, 2009, at 1:24 PM, Dave Clements, GMOD Help Desk wrote:

> Kate,
>
> Well, I'm glad you got it working, but database corruption does not
> make me feel warm and fuzzy  :-(
>
> A couple of questions:
> 1. Have other people hit this problem with a GFF2 load causing MySQL
> database corruption?
> 2. Which versions of MySQL and the load script are you using?
>
> If your site isn't relatively current with both then I would consider
> upgrading (particularly MySQL) and see if the problem goes away.
>
> Thanks,
>
> Dave C.
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
> On Thu, Feb 12, 2009 at 10:01 AM, Kate McGee <mcgeekm at mail.nih.gov>  
> wrote:
>> 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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>>>>
>>>>
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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
>>
>>
>>
>>
>>
>>


--------------------------------
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