<div dir="ltr">Oh no! I've never seen a memory problem before. How long a time elapses between the original loading message and the first Out of memory! message?<br><br>Lincoln<br><br><div class="gmail_quote">On Tue, Sep 23, 2008 at 1:25 PM, Zhiliang Hu <span dir="ltr"><<a href="mailto:zhu@iastate.edu">zhu@iastate.edu</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;">
<div>
Scott,<br><br>
I decide to take an "easier" approach as a start - I will try
to load NCBI and UCSC cattle genomes to GBrowse. Once that works, I
can move on with more customized data sets.<br><br>
I have following questions in doing that:<br><br>
1.<br>
A technical one: When I try to load a cattle chromosome using your
'load_genbank.pl', I got a memory problem (there is 8 GB RAM on the
machine - I bet there must a work around?)<br><br>
> load_genbank.pl --create -dsn dbi:mysql:gb_cattle -user --pass
--accession NC_007320<br>
Loading NC_007320...<br>
Out of memory!<br>
Out of memory!<br>
Out of memory!<br>
Segmentation fault (core dumped)<br><br>
2.<br>
Can I load all chromosomes into one database? Or should I create
separate databases for each chromosome? (I assume the former but not
sure).<br><br>
3.<br>
If I also bring in UCSC golden tracks, should I set up a different
database, Or can I put them into one db, naming UCSC chromosomes a little
differently?<br><br>
Thank you,<br><br>
Zhiliang<br><br>
<br>
<font color="#808080">--<br>
Zhi-Liang Hu (PhD)<br>
Associate Scientist,<br>
Department of Animal Science,<br>
Center for Integrated Animal Genomics,<br>
National Animal Genome Research Program,<br>
Iowa State University<br>
Tel: 901-759-0643<br>
Mob: 901-212-2820<br>
Web:
<a href="http://www.animalgenome.org/" target="_blank">
http://www.animalgenome.org<br><br>
</a></font><tt><font color="#808080" face="Comic Sans MS">"Not
everything that counts can be counted, and<br>
not everything that can be counted
counts."</font></tt><font color="#808080"><i> </i></font></div>
</blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br><br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>416 673-8514<br>Assistant: Stacey Quinn <<a href="mailto:Stacey.Quinn@oicr.on.ca">Stacey.Quinn@oicr.on.ca</a>><br>
<br>Cold Spring Harbor Laboratory<br>1 Bungtown Road<br>Cold Spring Harbor, NY 11724 USA<br>(516) 367-8380 <br>Assistant: Sandra Michelsen <<a href="mailto:michelse@cshl.edu">michelse@cshl.edu</a>><br>
</div>