[Gmod-help] get a new GBrowse to work

Zhiliang Hu zhu at iastate.edu
Mon Sep 29 23:21:45 EDT 2008 

Scott - Thanks for the follow up.
I am multi-tasking - will get back to it soon! ;-)

Zhiliang

At 11:17 PM 9/29/2008 -0400, Scott Cain wrote:
>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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