[Gmod-help] get a new GBrowse to work

Thu Sep 25 16:00:00 EDT 2008

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