[Gmod-help] get a new GBrowse to work

[Scott Cain]

There seems to be a problem with BioPerl related to getting the
sequence directly from GenBank: if I download NC_007320 and then run

   bp_genbank2gff.pl --file NC_007320.gbk  --dsn dbi:mysql:test --create

it works fine in a couple of seconds.  If however I run

  bp_genbank2gff.pl --accession NC_007320  --dsn dbi:mysql:test --create

I get these two lines over and over again as it runs for a long time
(I'm letting it go now so I can see how long it will take and what
will eventually happen):

Use of uninitialized value in pattern match (m//) at
/usr/local/share/perl/5.8.8/Bio/SeqIO/genbank.pm line 663, <GEN1> line
115.
Use of uninitialized value in pattern match (m//) at
/usr/local/share/perl/5.8.8/Bio/SeqIO/genbank.pm line 667, <GEN1> line
115.

Scott


On Wed, Sep 24, 2008 at 9:56 AM, Zhiliang Hu <zhu at iastate.edu> wrote:
> I repeated on the same machine (RHEL/RedHat Linux 2.4.21-20.ELsmp, 8GB RAM)
> - I counted 7 minutes before its quit on "Out of memory!" this time.
>
> I then installed Bioperl/GBrowse/etc last night on another machine (Linux
> CentOS, 8GB RAM), tried the same to run on background.
>
> This morning I found the processes died away without loading the db. I
> didn't find any core dump or else but only in the /tmp dir a file created
> shortly after I started it:
> http://nagrp2.ansci.iastate.edu/zhu/tmp/RJQApIbFbh.txt -- this doesn't seem
> to be right because on the browser it seems to be HUGE:
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=194719399&view=gbwithparts
>
> Zhiliang
>
>
> At 11:17 PM 9/23/2008 -0400, Lincoln Stein wrote:
>
> 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 >



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory