[Gmod-help] get a new GBrowse to work

Scott Cain cain.cshl at gmail.com
Mon Sep 29 23:17:28 EDT 2008 

I'm not sure off hand what the problem is--did you have any success
reworking your config file?

Scott

On Thu, Sep 25, 2008 at 4:00 PM, Dave Clements, GMOD Help Desk
<gmodhelp at googlemail.com> wrote:
> Hi Zhiliang,
>
> On Thu, Sep 25, 2008 at 9:32 AM, Zhiliang Hu <zhu at iastate.edu> wrote:
>> Thanks Dave,
>>
>> Web error logs -- Upon one web load, there are multiple lines of "Use of
>> uninitialized value" in some bioperl pm - I think that's fine.
>
> I tend to agree.
>
>> There are 3 errors in the end, probably need some attention:
>>
>> Odd number of elements in hash assignment at
>> /usr/local/lib/perl5/site_perl/5.8.5/i686-linux/Bio/Graphics/Browser/Util.pm
>> line 404.
>>
>> Odd number of elements in hash assignment at
>> /usr/local/lib/perl5/site_perl/5.8.5/Bio/DB/GFF/Util/Rearrange.pm line 83.
>>
>> -- It might be wrong input data? For that I think I will first take Scott's
>> approach to make sure input data is fine unless there are known issues?
>
> I have no idea if these would cause the problems you are seeing.  I
> find that when in doubt, always take Scott's approach.  :-)
>
>> Bio::Graphics::BrowserConfig=HASH(0x8d48380) at
>> /usr/local/lib/perl5/site_perl/5.8.5/i686-linux/Bio/Graphics/Browser.pm line
>> 587.
>>
>> -- I am not sure what it complains (a hash reference?)
>
> I don't know the code, but this error and the previous two seem like
> errors waiting to happen.  Lincoln, Scott: any opinions on that?
>
> Thanks,
>
> Dave C.
>
>> Zhiliang
>>
>>
>> At 07:51 AM 9/25/2008 -0600, Dave Clements, GMOD Help Desk wrote:
>>
>> Hi Zhiliang,
>>
>> Can you look at your apache error log and see what errors (if any) it
>> has?  It is often easier to come at from that end, rather than
>> manually checking config files.
>>
>> Also, FYI, animalgenome.org was down last night around midnight central
>> time.
>>
>> Thanks,
>>
>> Dave C.
>>
>> On Wed, Sep 24, 2008 at 2:55 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
>>> Hi Scott,
>>>
>>> I used ncbi powerscript to download the chromosome genbank file (it took 2
>>> hrs 10 min) then used your bp_genbank2gff.pl to load db.  Looks like the
>>> tables are populated:
>>>
>>> o fattribute ( 13 records )
>>> o fattribute_to_feature ( 7782 records )
>>> o fdata ( 10939 records )
>>> o fdna ( 44259 records )
>>> o fgroup ( 1953 records )
>>> o fmeta ( 4 records )
>>> o ftype ( 8 records )
>>>
>>> but I still cannot bring up the graphs:
>>> http://www.animalgenome.org/cgi-bin/gbrowse/cattle/
>>>
>>> Could you help to see if I have any key part missing from the config file:
>>> http://www.animalgenome.org/hu/share/scott/cow.conf
>>>
>>> Thank you,
>>>
>>> Zhiliang
>>>
>>>
>>> At 10:33 AM 9/24/2008 -0400, Scott Cain wrote:
>>>
>>> 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
>>
>>
>>
>> --
>> Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>
>
> --
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>



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

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