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

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


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

*) 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:

Best wishes,


On 05/31/2012 07:49 PM, abel huang wrote:
> Hi,Seth
>     I load GO database into my local mysql datbase by perl script "".The table list is in attachment file.
>     I use perl script ' -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>
> 收件人: "abel huang" <abelhuang at>
> 抄送: go-software at, "GO Help List" <gohelp at>
> 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
> 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 "".
>>     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

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