[Gmod-help] get a new GBrowse to work

[Zhiliang Hu]

Let me see ... about 4-5 minutes, then a core dumped (~3GB).
Seven lines of "Out of memory!" - all came out at once.

Zhiliang

At 10:13 PM 9/23/2008 -0400, Lincoln Stein wrote:
>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?
>
>Lincoln
>
>On Tue, Sep 23, 2008 at 1:25 PM, Zhiliang Hu <<mailto:zhu at iastate.edu>zhu at iastate.edu> wrote:
>Scott,
>
>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.
>
>I have following questions in doing that:
>
>1.
>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?)
>
>> load_genbank.pl --create -dsn dbi:mysql:gb_cattle -user --pass --accession NC_007320
>Loading NC_007320...
>Out of memory!
>Out of memory!
>Out of memory!
>Segmentation fault (core dumped)
>
>2.
>Can I load all chromosomes into one database?  Or should I create separate databases for each chromosome? (I assume the former but not sure).
>
>3.
>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?
>
>Thank you,
>
>Zhiliang
>
>
>--
>Zhi-Liang Hu (PhD)
>Associate Scientist,
>Department of Animal Science,
>Center for Integrated Animal Genomics,
>National Animal Genome Research Program,
>Iowa State University
>Tel: 901-759-0643
>Mob: 901-212-2820
>Web: <http://www.animalgenome.org/>http://www.animalgenome.org
>
>"Not everything that counts can be counted, and
>    not everything that can be counted counts." 
>
>
>
>
>-- 
>Lincoln D. Stein
>
>Ontario Institute for Cancer Research
>101 College St., Suite 800
>Toronto, ON, Canada M5G0A3
>416 673-8514
>Assistant: Stacey Quinn <<mailto:Stacey.Quinn at oicr.on.ca>Stacey.Quinn at oicr.on.ca>
>
>Cold Spring Harbor Laboratory
>1 Bungtown Road
>Cold Spring Harbor, NY 11724 USA
>(516) 367-8380 
>Assistant: Sandra Michelsen <<mailto:michelse at cshl.edu>michelse at cshl.edu>