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

[Lincoln Stein]

Database corruption shouldn't happen under any circumstances -- it shouldn't
be possible for a client program, like Perl, to corrupt the tables. However,
if you are using the bulk loader, I can imagine there might be heavy-load
related problems if the network connection is flaky or you are using a
database whose tables are mounted via NFS.

Lincoln

On Thu, Feb 12, 2009 at 1:41 PM, Kate McGee <mcgeekm at mail.nih.gov> wrote:

> 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
>
>
>
>
>
>


-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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