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I repeated on the same machine (RHEL/RedHat Linux 2.4.21-20.ELsmp, 8GB
RAM) - I counted 7 minutes before its quit on "Out of memory!"
this time.<br><br>
I then installed Bioperl/GBrowse/etc last night on another machine (Linux
CentOS, 8GB RAM), tried the same to run on background.<br><br>
This morning I found the processes died away without loading the db. I
didn't find any core dump or else but only in the /tmp dir a file created
shortly after I started it:
<a href="http://nagrp2.ansci.iastate.edu/zhu/tmp/RJQApIbFbh.txt" eudora="autourl">
http://nagrp2.ansci.iastate.edu/zhu/tmp/RJQApIbFbh.txt</a> -- this
doesn't seem to be right because on the browser it seems to be HUGE:
<a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=194719399&view=gbwithparts" eudora="autourl">
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=194719399&view=gbwithparts</a>
<br><br>
Zhiliang<br><br>
<br>
At 11:17 PM 9/23/2008 -0400, Lincoln Stein wrote:<br>
<blockquote type=cite class=cite cite="">It may take a long time to run -
try overnight.<br><br>
Lincoln<br><br>
On Tue, Sep 23, 2008 at 10:46 PM, Scott Cain
<<a href="mailto:cain.cshl@gmail.com">cain.cshl@gmail.com</a>>
wrote:<br>
<dl>
<dd>When I ran it, it spun it's wheels for a long time (30+ minutes) and
I<br>
<dd>killed it. I tried the analagous thing with
bp_genbank2gff.pl and<br>
<dd>had to kill it too. I thought it was a problem with bioperl
until<br>
<dd>just now, when I tried it with an E coli chromosome from genbank
and<br>
<dd>it worked fine (it ran a couple of minutes).<br>
<font color="#888888"><br>
<dd>Scott<br>
</font><br><br>
<dd>On Tue, Sep 23, 2008 at 10:13 PM, Lincoln Stein
<<a href="mailto:lincoln.stein@gmail.com">lincoln.stein@gmail.com</a>
> wrote:<br>
<dd>> Oh no! I've never seen a memory problem before. How long a time
elapses<br>
<dd>> between the original loading message and the first Out of
memory! message?<br>
<dd>><br>
<dd>> Lincoln<br>
<dd>><br>
<dd>> On Tue, Sep 23, 2008 at 1:25 PM, Zhiliang Hu
<<a href="mailto:zhu@iastate.edu">zhu@iastate.edu</a>> wrote:<br>
<dd>>><br>
<dd>>> Scott,<br>
<dd>>><br>
<dd>>> I decide to take an "easier" approach as a start -
I will try to load NCBI<br>
<dd>>> and UCSC cattle genomes to GBrowse. Once that works, I
can move on with<br>
<dd>>> more customized data sets.<br>
<dd>>><br>
<dd>>> I have following questions in doing that:<br>
<dd>>><br>
<dd>>> 1.<br>
<dd>>> A technical one: When I try to load a cattle chromosome
using your<br>
<dd>>> 'load_genbank.pl', I got a memory problem (there is 8 GB RAM
on the machine<br>
<dd>>> - I bet there must a work around?)<br>
<dd>>><br>
<dd>>> > load_genbank.pl --create -dsn dbi:mysql:gb_cattle -user
--pass<br>
<dd>>> > --accession NC_007320<br>
<dd>>> Loading NC_007320...<br>
<dd>>> Out of memory!<br>
<dd>>> Out of memory!<br>
<dd>>> Out of memory!<br>
<dd>>> Segmentation fault (core dumped)<br>
<dd>>><br>
<dd>>> 2.<br>
<dd>>> Can I load all chromosomes into one database? Or
should I create separate<br>
<dd>>> databases for each chromosome? (I assume the former but not
sure).<br>
<dd>>><br>
<dd>>> 3.<br>
<dd>>> If I also bring in UCSC golden tracks, should I set up a
different<br>
<dd>>> database, Or can I put them into one db, naming UCSC
chromosomes a little<br>
<dd>>> differently?<br>
<dd>>><br>
<dd>>> Thank you,<br>
<dd>>><br>
<dd>>> Zhiliang<br>
<dd>>><br>
<dd>>><br>
<dd>>> --<br>
<dd>>> Zhi-Liang Hu (PhD)<br>
<dd>>> Associate Scientist,<br>
<dd>>> Department of Animal Science,<br>
<dd>>> Center for Integrated Animal Genomics,<br>
<dd>>> National Animal Genome Research Program,<br>
<dd>>> Iowa State University<br>
<dd>>> Tel: 901-759-0643<br>
<dd>>> Mob: 901-212-2820<br>
<dd>>> Web:
<a href="http://www.animalgenome.org">http://www.animalgenome.org</a><br>
<dd>>><br>
<dd>>> "Not everything that counts can be counted, and<br>
<dd>>> not everything that can be counted
counts."<br>
<dd>><br>
<dd>><br>
<dd>> --<br>
<dd>> Lincoln D. Stein<br>
<dd>><br>
<dd>> Ontario Institute for Cancer Research<br>
<dd>> 101 College St., Suite 800<br>
<dd>> Toronto, ON, Canada M5G0A3<br>
<dd>> 416 673-8514<br>
<dd>> Assistant: Stacey Quinn
<<a href="mailto:Stacey.Quinn@oicr.on.ca">Stacey.Quinn@oicr.on.ca</a>
><br>
<dd>><br>
<dd>> Cold Spring Harbor Laboratory<br>
<dd>> 1 Bungtown Road<br>
<dd>> Cold Spring Harbor, NY 11724 USA<br>
<dd>> (516) 367-8380<br>
<dd>> Assistant: Sandra Michelsen
<<a href="mailto:michelse@cshl.edu">michelse@cshl.edu</a>><br>
<dd>><br><br>
<br><br>
<dd>--<br>
<dd>
------------------------------------------------------------------------<br>
<dd>Scott Cain, Ph. D.
<a href="mailto:cain.cshl@gmail.com">cain.cshl@gmail.com</a><br>
<dd>GMOD Coordinator (<a href="http://gmod.org/">http://gmod.org/</a>)
216-392-3087<br>
<dd>Cold Spring Harbor Laboratory<br><br>
</dl><br><br>
<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>
></blockquote></body>
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