[Gmod-help] get a new GBrowse to work

[Scott Cain]

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