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Thanks Dave,<br><br>
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.<br><br>
There are 3 errors in the end, probably need some attention:<br><br>
<font color="#808080">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.<br><br>
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.<br><br>
</font>-- 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?<br><br>
<font color="#808080">Bio::Graphics::BrowserConfig=HASH(0x8d48380) at
/usr/local/lib/perl5/site_perl/5.8.5/i686-linux/Bio/Graphics/Browser.pm
line 587.<br><br>
</font>-- I am not sure what it complains (a hash reference?)<br><br>
Zhiliang<br><br>
<br>
At 07:51 AM 9/25/2008 -0600, Dave Clements, GMOD Help Desk wrote:<br>
<blockquote type=cite class=cite cite="">Hi Zhiliang,<br><br>
Can you look at your apache error log and see what errors (if any)
it<br>
has? It is often easier to come at from that end, rather than<br>
manually checking config files.<br><br>
Also, FYI, animalgenome.org was down last night around midnight central
time.<br><br>
Thanks,<br><br>
Dave C.<br><br>
On Wed, Sep 24, 2008 at 2:55 PM, Zhiliang Hu <zhu@iastate.edu>
wrote:<br>
> Hi Scott,<br>
><br>
> I used ncbi powerscript to download the chromosome genbank file (it
took 2<br>
> hrs 10 min) then used your bp_genbank2gff.pl to load db. Looks
like the<br>
> tables are populated:<br>
><br>
> o fattribute ( 13 records )<br>
> o fattribute_to_feature ( 7782 records )<br>
> o fdata ( 10939 records )<br>
> o fdna ( 44259 records )<br>
> o fgroup ( 1953 records )<br>
> o fmeta ( 4 records )<br>
> o ftype ( 8 records )<br>
><br>
> but I still cannot bring up the graphs:<br>
>
<a href="http://www.animalgenome.org/cgi-bin/gbrowse/cattle/" eudora="autourl">
http://www.animalgenome.org/cgi-bin/gbrowse/cattle/</a><br>
><br>
> Could you help to see if I have any key part missing from the config
file:<br>
>
<a href="http://www.animalgenome.org/hu/share/scott/cow.conf" eudora="autourl">
http://www.animalgenome.org/hu/share/scott/cow.conf</a><br>
><br>
> Thank you,<br>
><br>
> Zhiliang<br>
><br>
><br>
> At 10:33 AM 9/24/2008 -0400, Scott Cain wrote:<br>
><br>
> There seems to be a problem with BioPerl related to getting the<br>
> sequence directly from GenBank: if I download NC_007320 and then
run<br>
><br>
> bp_genbank2gff.pl --file NC_007320.gbk --dsn
dbi:mysql:test --create<br>
><br>
> it works fine in a couple of seconds. If however I run<br>
><br>
> bp_genbank2gff.pl --accession NC_007320 --dsn
dbi:mysql:test --create<br>
><br>
> I get these two lines over and over again as it runs for a long
time<br>
> (I'm letting it go now so I can see how long it will take and
what<br>
> will eventually happen):<br>
><br>
> Use of uninitialized value in pattern match (m//) at<br>
> /usr/local/share/perl/5.8.8/Bio/SeqIO/genbank.pm line 663,
<GEN1> line<br>
> 115.<br>
> Use of uninitialized value in pattern match (m//) at<br>
> /usr/local/share/perl/5.8.8/Bio/SeqIO/genbank.pm line 667,
<GEN1> line<br>
> 115.<br>
><br>
> Scott<br>
><br>
><br>
> On Wed, Sep 24, 2008 at 9:56 AM, Zhiliang Hu <zhu@iastate.edu>
wrote:<br>
>> I repeated on the same machine (RHEL/RedHat Linux
2.4.21-20.ELsmp, 8GB<br>
>> RAM)<br>
>> - I counted 7 minutes before its quit on "Out of
memory!" this time.<br>
>><br>
>> I then installed Bioperl/GBrowse/etc last night on another
machine (Linux<br>
>> CentOS, 8GB RAM), tried the same to run on background.<br>
>><br>
>> This morning I found the processes died away without loading the
db. I<br>
>> didn't find any core dump or else but only in the /tmp dir a
file created<br>
>> shortly after I started it:<br>
>>
<a href="http://nagrp2.ansci.iastate.edu/zhu/tmp/RJQApIbFbh.txt" eudora="autourl">
http://nagrp2.ansci.iastate.edu/zhu/tmp/RJQApIbFbh.txt</a> -- this
doesn't<br>
>> seem<br>
>> to be right because on the browser it seems to be HUGE:<br>
>><br>
>>
<a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=194719399&view=gbwithparts" eudora="autourl">
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=194719399&view=gbwithparts</a>
<br>
>><br>
>> Zhiliang<br>
>><br>
>><br>
>> At 11:17 PM 9/23/2008 -0400, Lincoln Stein wrote:<br>
>><br>
>> It may take a long time to run - try overnight.<br>
>><br>
>> Lincoln<br>
>><br>
>> On Tue, Sep 23, 2008 at 10:46 PM, Scott Cain
<cain.cshl@gmail.com> wrote:<br>
>> 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>
>><br>
>> Scott<br>
>><br>
>><br>
>> On Tue, Sep 23, 2008 at 10:13 PM, Lincoln Stein
<lincoln.stein@gmail.com ><br>
>> 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!<br>
>>> message?<br>
>>><br>
>>> Lincoln<br>
>>><br>
>>> On Tue, Sep 23, 2008 at 1:25 PM, Zhiliang Hu
<zhu@iastate.edu> wrote:<br>
>>>><br>
>>>> Scott,<br>
>>>><br>
>>>> I decide to take an "easier" approach as a
start - I will try to load<br>
>>>> 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<br>
>>>> 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<br>
>>>> 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<br>
>>>> 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/" eudora="autourl">
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 <Stacey.Quinn@oicr.on.ca
><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 <michelse@cshl.edu><br>
>>><br>
>><br>
>><br>
>><br>
>> --<br>
>>
------------------------------------------------------------------------<br>
>> Scott Cain, Ph. D. cain.cshl@gmail.com<br>
>> GMOD Coordinator
(<a href="http://gmod.org/" eudora="autourl">http://gmod.org/</a>)
216-392-3087<br>
>> Cold Spring Harbor Laboratory<br>
>><br>
>><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 <Stacey.Quinn@oicr.on.ca ><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 <michelse@cshl.edu ><br>
><br>
><br>
><br>
> --<br>
>
------------------------------------------------------------------------<br>
> Scott Cain, Ph. D. cain.cshl@gmail.com<br>
> GMOD Coordinator
(<a href="http://gmod.org/" eudora="autourl">http://gmod.org/</a>)
216-392-3087<br>
> Cold Spring Harbor Laboratory<br><br>
<br><br>
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