[Gmod-help] get a new GBrowse to work

[Lincoln Stein]

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
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Cold Spring Harbor Laboratory
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