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[go-helpdesk] [go-software] AmiGO1.8 running error

Seth Carbon sjcarbon at lbl.gov
Fri Jun 1 12:57:15 PDT 2012


Abel,

Again, there is not enough information here to really do any debugging
remotely--without a specific error message on a specific page (e.g. this
link on the the page with URL gives nothing), it is guesswork.

The next few things you might want to try are:

*) Check to make sure that the database is properly populated, maybe:
SELECT COUNT(*) FROM gene_product_homolset

*) Verbose output in AmiGO while running on problematic pages (described
previously).

*) You would probably want to run AmiGO (probably amigo) from the
command line with the same arguments as are used in the URL (described
previously; also see: http://search.cpan.org/dist/CGI/lib/CGI.pm#DEBUGGING).

Best wishes,

-Seth


On 05/31/2012 07:49 PM, abel huang wrote:
> Hi,Seth
> 
>     I load GO database into my local mysql datbase by perl script "go_db_install.pl".The table list is in attachment file.
> 
>     I use perl script 'refresh.pl -s -g -p -l' to generate cache file after install AmiGO1.8.
> 
>     But Homolog Annotations link do not work.
> 
>     I run the command line "./amigo" in cgi-bin directory, there is no error, it print tab "Tools & Resources" html.
> 
>     Can you give me some help for solve this problem?
> 
> ----- 原始邮件 -----
> 发件人: "Seth Carbon" <sjcarbon at lbl.gov>
> 收件人: "abel huang" <abelhuang at tilsi.org>
> 抄送: go-software at mailman.stanford.edu, "GO Help List" <gohelp at genome.stanford.edu>
> 发送时间: 星期四, 2012年 5 月 31日 上午 5:58:29
> 主题: Re: [go-software] AmiGO1.8 running error
> 
> Abel,
> 
> Unfortunately, this is not a lot to go on--I'm not sure if the problem
> you're having is with the homolog sets specifically or AmiGO in general.
> Although at first blush it could be a slowness/database issue.
> 
> You may find it helpful to run AmiGO off of the command line in the
> cgi-bin directory (./amigo "YOUR PARAMETERS HERE"), where it cannot
> timeout. Also, you probably would want to enable debugging output (see
> AMIGO_VERBOSE at:
> http://wiki.geneontology.org/index.php/AmiGO_Manual:_Installation_1.8#Variable_Meanings)
> to help diagnose the issue.
> 
> Hopefully these will get you more information with which you can
> troubleshoot your problem.
> 
> Best wishes,
> 
> -Seth
> 
> 
> On 05/29/2012 08:28 PM, abel huang wrote:
>> Hi,All
>>     I install AmiGO 1.8 step by step from "http://wiki.geneontology.org/index.php/AmiGO_Manual:_Installation_1.8".
>>     T load go assocdb into my mysql database.
>>
>>     But Homolog Annotations link do not work, and the message follow : Timeout waiting for output from CGI script /var/www/cgi-bin/amigo/amigo.
>>
>>     I do not  konw why. Hope you can help for me?
>>
>>
>>     thank you very much.
>> _______________________________________________
>> go-software mailing list
>> go-software at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/go-software
>>
>>



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