[Gmod-help] get a new GBrowse to work

[Lincoln Stein]

It may take a long time to run - try overnight.

Lincoln

On Tue, Sep 23, 2008 at 10:46 PM, Scott Cain <cain.cshl at gmail.com> wrote:

> When I ran it, it spun it's wheels for a long time (30+ minutes) and I
> killed it.   I tried the analagous thing with bp_genbank2gff.pl and
> had to kill it too.  I thought it was a problem with bioperl until
> just now, when I tried it with an E coli chromosome from genbank and
> it worked fine (it ran a couple of minutes).
>
> Scott
>
>
> On Tue, Sep 23, 2008 at 10:13 PM, Lincoln Stein <lincoln.stein at gmail.com>
> 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 <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
> >>
> >> "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 <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 <michelse at cshl.edu>
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. cain.cshl at gmail.com
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Cold Spring Harbor Laboratory
>



-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <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 <michelse at cshl.edu>
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