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.<br>
<br>Lincoln<br><br><div class="gmail_quote">On Thu, Feb 12, 2009 at 1:41 PM, Kate McGee <span dir="ltr"><<a href="mailto:mcgeekm@mail.nih.gov">mcgeekm@mail.nih.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Database corruption doesn't make me feel warm and fuzzy either!<br>
<br>
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<br>
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?<br>
<br>
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?<br>
<br>
Thanks<br><font color="#888888">
Kate</font><div><div></div><div class="Wj3C7c"><br>
<br>
<br>
On Feb 12, 2009, at 1:24 PM, Dave Clements, GMOD Help Desk wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Kate,<br>
<br>
Well, I'm glad you got it working, but database corruption does not<br>
make me feel warm and fuzzy :-(<br>
<br>
A couple of questions:<br>
1. Have other people hit this problem with a GFF2 load causing MySQL<br>
database corruption?<br>
2. Which versions of MySQL and the load script are you using?<br>
<br>
If your site isn't relatively current with both then I would consider<br>
upgrading (particularly MySQL) and see if the problem goes away.<br>
<br>
Thanks,<br>
<br>
Dave C.<br>
<br>
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On Thu, Feb 12, 2009 at 10:01 AM, Kate McGee <<a href="mailto:mcgeekm@mail.nih.gov" target="_blank">mcgeekm@mail.nih.gov</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Actually I ran the mySQL "isamchk -r" command and it repaired the table.<br>
There was an issue with the indexing.<br>
<br>
The problem is that every time I load a large amount of genotype data (I<br>
have been doing it one chromosome at a time), it corrupts the table again.<br>
So I am going to finish loading it, run isamchk and see if it can repair<br>
the table again with even more data in it.<br>
<br>
Kate<br>
<br>
<br>
On Feb 12, 2009, at 12:51 PM, Dave Clements, GMOD Help Desk wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Kate,<br>
<br>
Were you ever successful at loading the data? My usual problem with<br>
large datasets is running out of space on one of my disks.<br>
<br>
If not, can you post the specific error you are getting?<br>
<br>
Thanks,<br>
<br>
Dave C.<br>
<br>
<br>
Was this helpful? Let us know at <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br>
<br>
<br>
<br>
On Fri, Jan 30, 2009 at 6:21 AM, Erick Antezana <<a href="mailto:erant@psb.vib-ugent.be" target="_blank">erant@psb.vib-ugent.be</a>><br>
wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
A colleague just told me, he was able to load the hapmap stuff in GBrowse<br>
1.69 too.<br>
<br>
Erick<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
I have a very large amount of genotype data (~2000 individuals,<br>
700,000 SNPs) that I would like to load into our mysql database so<br>
that it can be downloaded from our browser. After loading three<br>
chromosomes our mysql database crashed. It is being loaded into the<br>
fattribute_to_feature table in a text field. Has anyone had success<br>
storing/loading this much data?<br>
<br>
Thanks,<br>
Kate<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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<br>
--------------------------------<br>
Kate McGee, Ph.D.<br>
Postdoctoral Fellow<br>
National Cancer Institute at Frederick<br>
Office: Building 559, Room 5<br>
Phone: (301) 846-5425<br>
<a href="mailto:mcgeekm@mail.nih.gov" target="_blank">mcgeekm@mail.nih.gov</a><br>
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--------------------------------<br>
Kate McGee, Ph.D.<br>
Postdoctoral Fellow<br>
National Cancer Institute at Frederick<br>
Office: Building 559, Room 5<br>
Phone: (301) 846-5425<br>
<a href="mailto:mcgeekm@mail.nih.gov" target="_blank">mcgeekm@mail.nih.gov</a><br>
<br>
<br>
<br>
<br>
<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>
416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br>