<div dir="ltr">It may take a long time to run - try overnight.<br><br>Lincoln<br><br><div class="gmail_quote">On Tue, Sep 23, 2008 at 10:46 PM, Scott Cain <span dir="ltr"><<a href="mailto:cain.cshl@gmail.com">cain.cshl@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">When I ran it, it spun it's wheels for a long time (30+ minutes) and I<br>
killed it. I tried the analagous thing with bp_genbank2gff.pl and<br>
had to kill it too. I thought it was a problem with bioperl until<br>
just now, when I tried it with an E coli chromosome from genbank and<br>
it worked fine (it ran a couple of minutes).<br>
<font color="#888888"><br>
Scott<br>
</font><div><div></div><div class="Wj3C7c"><br>
<br>
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>
> Oh no! I've never seen a memory problem before. How long a time elapses<br>
> between the original loading message and the first Out of memory! message?<br>
><br>
> Lincoln<br>
><br>
> On Tue, Sep 23, 2008 at 1:25 PM, Zhiliang Hu <<a href="mailto:zhu@iastate.edu">zhu@iastate.edu</a>> wrote:<br>
>><br>
>> Scott,<br>
>><br>
>> I decide to take an "easier" approach as a start - I will try to load NCBI<br>
>> and UCSC cattle genomes to GBrowse. Once that works, I can move on with<br>
>> more customized data sets.<br>
>><br>
>> I have following questions in doing that:<br>
>><br>
>> 1.<br>
>> A technical one: When I try to load a cattle chromosome using your<br>
>> 'load_genbank.pl', I got a memory problem (there is 8 GB RAM on the machine<br>
>> - I bet there must a work around?)<br>
>><br>
>> > load_genbank.pl --create -dsn dbi:mysql:gb_cattle -user --pass<br>
>> > --accession NC_007320<br>
>> Loading NC_007320...<br>
>> Out of memory!<br>
>> Out of memory!<br>
>> Out of memory!<br>
>> Segmentation fault (core dumped)<br>
>><br>
>> 2.<br>
>> Can I load all chromosomes into one database? Or should I create separate<br>
>> databases for each chromosome? (I assume the former but not sure).<br>
>><br>
>> 3.<br>
>> If I also bring in UCSC golden tracks, should I set up a different<br>
>> database, Or can I put them into one db, naming UCSC chromosomes a little<br>
>> differently?<br>
>><br>
>> Thank you,<br>
>><br>
>> Zhiliang<br>
>><br>
>><br>
>> --<br>
>> Zhi-Liang Hu (PhD)<br>
>> Associate Scientist,<br>
>> Department of Animal Science,<br>
>> Center for Integrated Animal Genomics,<br>
>> National Animal Genome Research Program,<br>
>> Iowa State University<br>
>> Tel: 901-759-0643<br>
>> Mob: 901-212-2820<br>
>> Web: <a href="http://www.animalgenome.org" target="_blank">http://www.animalgenome.org</a><br>
>><br>
>> "Not everything that counts can be counted, and<br>
>> not everything that can be counted counts."<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>><br>
><br>
<br>
<br>
<br>
</div></div><div><div></div><div class="Wj3C7c">--<br>
------------------------------------------------------------------------<br>
Scott Cain, Ph. D. <a href="mailto:cain.cshl@gmail.com">cain.cshl@gmail.com</a><br>
GMOD Coordinator (<a href="http://gmod.org/" target="_blank">http://gmod.org/</a>) 216-392-3087<br>
Cold Spring Harbor Laboratory<br>
</div></div></blockquote></div><br><br clear="all"><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>><br>
</div>