a question of Gbrowse 2

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a question of Gbrowse 2

zhuang chao
Greeting ,

I have my Gbrowse 2.0 attached to a chado postgres database .

Apache fails to load and give the following error in the error.log :

===============================================================================

[Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined value
at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.

[Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse

================================================================================

How can I solve the problem. could  you give me a help ?  Thank you very much !

here is my database settings :

**********************************************

[four_viruses:database]
db_adaptor    = Bio::DB::Das::Chado

db_args       = -dsn
dbi:Pg:dbname=four_viruses;host=192.168.30.213;port=5432
                -user zc
                -pass  123456

**********************************************

zhuangchao



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Re: a question of Gbrowse 2

Scott Cain
Hi Zhuang,

First, make sure that you have the most recent version of
Bio::DB::Das::Chado; it is 0.26.

Next, if you loaded Chado with the --noexon flag with the gff3 loader,
you need the '-inferCDS 1' option added to you db_args.  See `perldoc
Bio::DB::Das::Chado` for more information on that and other
constructor options.

Scott


2010/6/8 zhuangchao <[hidden email]>:

> Greeting ,
>
> I have my Gbrowse 2.0 attached to a chado postgres database .
>
> Apache fails to load and give the following error in the error.log :
>
> ===============================================================================
>
> [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined value
> at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
>
> [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
>
> ================================================================================
>
> How can I solve the problem. could  you give me a help ?  Thank you very much !
>
> here is my database settings :
>
> **********************************************
>
> [four_viruses:database]
> db_adaptor    = Bio::DB::Das::Chado
>
> db_args       = -dsn
> dbi:Pg:dbname=four_viruses;host=192.168.30.213;port=5432
>                -user zc
>                -pass  123456
>
> **********************************************
>
> zhuangchao
>
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: a question of Gbrowse 2

zhuang chao
hi  Scott ,

I updated Bio::DB::Das::Chado to 0.26 and  added

'-inferCDS 1' option to the  db_args of the  Gbrowse 2 .

I  loaded  Chado with  the --noexon flag with the gff3 loader .

But the question still exist. I think that may be a bug of

Gbrowse 2 .


===============================================================================

[Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined
 value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.

[Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse


================================================================================


could  you give me a help ?  Thank you very much !




On Tue, 2010-06-08 at 09:45 -0400, Scott Cain wrote:

> Hi Zhuang,
>
> First, make sure that you have the most recent version of
> Bio::DB::Das::Chado; it is 0.26.
>
> Next, if you loaded Chado with the --noexon flag with the gff3 loader,
> you need the '-inferCDS 1' option added to you db_args.  See `perldoc
> Bio::DB::Das::Chado` for more information on that and other
> constructor options.
>
> Scott
>
>
> 2010/6/8 zhuangchao <[hidden email]>:
> > Greeting ,
> >
> > I have my Gbrowse 2.0 attached to a chado postgres database .
> >
> > Apache fails to load and give the following error in the error.log :
> >
> > ===============================================================================
> >
> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined value
> > at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
> >
> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
> >
> > ================================================================================
> >
> > How can I solve the problem. could  you give me a help ?  Thank you very much !
> >
> > here is my database settings :
> >
> > **********************************************
> >
> > [four_viruses:database]
> > db_adaptor    = Bio::DB::Das::Chado
> >
> > db_args       = -dsn
> > dbi:Pg:dbname=four_viruses;host=192.168.30.213;port=5432
> >                -user zc
> >                -pass  123456
> >
> > **********************************************
> >
> > zhuangchao
> >
> >
> >
>
>
>



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Re: a question of Gbrowse 2

Scott Cain
Hi Zhuang,

Can you send the full configuration file that you are using with
Chado?  I'm wondering if one of your track configurations has a
problem.

Scott


On Tue, Jun 8, 2010 at 9:44 PM, zhuang chao <[hidden email]> wrote:

> hi  Scott ,
>
> I updated Bio::DB::Das::Chado to 0.26 and  added
>
> '-inferCDS 1' option to the  db_args of the  Gbrowse 2 .
>
> I  loaded  Chado with  the --noexon flag with the gff3 loader .
>
> But the question still exist. I think that may be a bug of
>
> Gbrowse 2 .
>
>
> ===============================================================================
>
> [Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined
>  value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
>
> [Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
>
>
> ================================================================================
>
>
> could  you give me a help ?  Thank you very much !
>
>
>
>
> On Tue, 2010-06-08 at 09:45 -0400, Scott Cain wrote:
>> Hi Zhuang,
>>
>> First, make sure that you have the most recent version of
>> Bio::DB::Das::Chado; it is 0.26.
>>
>> Next, if you loaded Chado with the --noexon flag with the gff3 loader,
>> you need the '-inferCDS 1' option added to you db_args.  See `perldoc
>> Bio::DB::Das::Chado` for more information on that and other
>> constructor options.
>>
>> Scott
>>
>>
>> 2010/6/8 zhuangchao <[hidden email]>:
>> > Greeting ,
>> >
>> > I have my Gbrowse 2.0 attached to a chado postgres database .
>> >
>> > Apache fails to load and give the following error in the error.log :
>> >
>> > ===============================================================================
>> >
>> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined value
>> > at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
>> >
>> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
>> >
>> > ================================================================================
>> >
>> > How can I solve the problem. could  you give me a help ?  Thank you very much !
>> >
>> > here is my database settings :
>> >
>> > **********************************************
>> >
>> > [four_viruses:database]
>> > db_adaptor    = Bio::DB::Das::Chado
>> >
>> > db_args       = -dsn
>> > dbi:Pg:dbname=four_viruses;host=192.168.30.213;port=5432
>> >                -user zc
>> >                -pass  123456
>> >
>> > **********************************************
>> >
>> > zhuangchao
>> >
>> >
>> >
>>
>>
>>
>
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: a question of Gbrowse 2

zhuang chao
hi Scott ,

The full configuration file is in the attachment.

Thank you very much !



On Tue, 2010-06-08 at 21:51 -0400, Scott Cain wrote:

> Hi Zhuang,
>
> Can you send the full configuration file that you are using with
> Chado?  I'm wondering if one of your track configurations has a
> problem.
>
> Scott
>
>
> On Tue, Jun 8, 2010 at 9:44 PM, zhuang chao <[hidden email]> wrote:
> > hi  Scott ,
> >
> > I updated Bio::DB::Das::Chado to 0.26 and  added
> >
> > '-inferCDS 1' option to the  db_args of the  Gbrowse 2 .
> >
> > I  loaded  Chado with  the --noexon flag with the gff3 loader .
> >
> > But the question still exist. I think that may be a bug of
> >
> > Gbrowse 2 .
> >
> >
> > ===============================================================================
> >
> > [Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined
> >  value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
> >
> > [Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
> >
> >
> > ================================================================================
> >
> >
> > could  you give me a help ?  Thank you very much !
> >
> >
> >
> >
> > On Tue, 2010-06-08 at 09:45 -0400, Scott Cain wrote:
> >> Hi Zhuang,
> >>
> >> First, make sure that you have the most recent version of
> >> Bio::DB::Das::Chado; it is 0.26.
> >>
> >> Next, if you loaded Chado with the --noexon flag with the gff3 loader,
> >> you need the '-inferCDS 1' option added to you db_args.  See `perldoc
> >> Bio::DB::Das::Chado` for more information on that and other
> >> constructor options.
> >>
> >> Scott
> >>
> >>
> >> 2010/6/8 zhuangchao <[hidden email]>:
> >> > Greeting ,
> >> >
> >> > I have my Gbrowse 2.0 attached to a chado postgres database .
> >> >
> >> > Apache fails to load and give the following error in the error.log :
> >> >
> >> > ===============================================================================
> >> >
> >> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined value
> >> > at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
> >> >
> >> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
> >> >
> >> > ================================================================================
> >> >
> >> > How can I solve the problem. could  you give me a help ?  Thank you very much !
> >> >
> >> > here is my database settings :
> >> >
> >> > **********************************************
> >> >
> >> > [four_viruses:database]
> >> > db_adaptor    = Bio::DB::Das::Chado
> >> >
> >> > db_args       = -dsn
> >> > dbi:Pg:dbname=four_viruses;host=192.168.30.213;port=5432
> >> >                -user zc
> >> >                -pass  123456
> >> >
> >> > **********************************************
> >> >
> >> > zhuangchao
> >> >
> >> >
> >> >
> >>
> >>
> >>
> >
> >
> >
>
>
>

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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
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four_viruses1.conf (3K) Download Attachment
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Re: a question of Gbrowse 2

zhuang chao
In reply to this post by Scott Cain
hi, Scott,

I am using the GBrowse 2.08  attached to a chado postgres database .

The full configuration file  is in the attachment.  

The   genbank and  gff3  file   is  in  the  attachment  ,too.

The command line of loading  gff3 file is following :
=======================================================================
perl /usr/local/bin/gmod_bulk_load_gff3.pl  --gfffile GU207834.gbk.gff
--organism 'Rabies virus' --dbname four_viruses --dbuser zc --dbpass
123456 --dbhost localhost --dbport 5432 --recreate_cache --noexon
=======================================================================

The url is  following:

http://192.168.30.213/cgi-bin/gb2/gbrowse/four_viruses1/?name=GU207834
=======================================================================

 Thank you very much !


**********************************************************************************

On Tue, 2010-06-08 at 21:51 -0400, Scott Cain wrote:

> Hi Zhuang,
>
> Can you send the full configuration file that you are using with
> Chado?  I'm wondering if one of your track configurations has a
> problem.
>
> Scott
>
>
> On Tue, Jun 8, 2010 at 9:44 PM, zhuang chao <[hidden email]> wrote:
> > hi  Scott ,
> >
> > I updated Bio::DB::Das::Chado to 0.26 and  added
> >
> > '-inferCDS 1' option to the  db_args of the  Gbrowse 2 .
> >
> > I  loaded  Chado with  the --noexon flag with the gff3 loader .
> >
> > But the question still exist. I think that may be a bug of
> >
> > Gbrowse 2 .
> >
> >
> > ===============================================================================
> >
> > [Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined
> >  value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
> >
> > [Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
> >
> >
> > ================================================================================
> >
> >
> > could  you give me a help ?  Thank you very much !
> >
> >
> >
> >
> > On Tue, 2010-06-08 at 09:45 -0400, Scott Cain wrote:
> >> Hi Zhuang,
> >>
> >> First, make sure that you have the most recent version of
> >> Bio::DB::Das::Chado; it is 0.26.
> >>
> >> Next, if you loaded Chado with the --noexon flag with the gff3 loader,
> >> you need the '-inferCDS 1' option added to you db_args.  See `perldoc
> >> Bio::DB::Das::Chado` for more information on that and other
> >> constructor options.
> >>
> >> Scott
> >>
> >>
> >> 2010/6/8 zhuangchao <[hidden email]>:
> >> > Greeting ,
> >> >
> >> > I have my Gbrowse 2.0 attached to a chado postgres database .
> >> >
> >> > Apache fails to load and give the following error in the error.log :
> >> >
> >> > ===============================================================================
> >> >
> >> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined value
> >> > at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
> >> >
> >> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
> >> >
> >> > ================================================================================
> >> >
> >> > How can I solve the problem. could  you give me a help ?  Thank you very much !
> >> >
> >> > here is my database settings :
> >> >
> >> > **********************************************
> >> >
> >> > [four_viruses:database]
> >> > db_adaptor    = Bio::DB::Das::Chado
> >> >
> >> > db_args       = -dsn
> >> > dbi:Pg:dbname=four_viruses;host=192.168.30.213;port=5432
> >> >                -user zc
> >> >                -pass  123456
> >> >
> >> > **********************************************
> >> >
> >> > zhuangchao
> >> >
> >> >
> >> >
> >>
> >>
> >>
> >
> >
> >
>
>
>

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GU207834.gbk (3K) Download Attachment
GU207834.gbk.gff (1K) Download Attachment
four_viruses1.conf (3K) Download Attachment
GBrowse.conf (6K) Download Attachment
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Re: a question of Gbrowse 2

Scott Cain
Hi Zhuang,

I won't have time to do any testing on this until later, but in the
meantime, I have a few suggestions:

* Remove tracks that you aren't using.  I'm reasonably sure you virus
data doesn't have any rRNA:sgd or long_terminal_repeat types.

* Fix the CDS track.  It has gene features as the parent of your CDS
features, but that is not the case.  The feature for your CDS track
should be mRNA (that way, it's telling GBrowse when you want a CDS
track that groups your CDS features on a given mRNA).

Scott


On Wed, Jun 9, 2010 at 6:15 AM, zhuang chao <[hidden email]> wrote:

> hi, Scott,
>
> I am using the GBrowse 2.08  attached to a chado postgres database .
>
> The full configuration file  is in the attachment.
>
> The   genbank and  gff3  file   is  in  the  attachment  ,too.
>
> The command line of loading  gff3 file is following :
> =======================================================================
> perl /usr/local/bin/gmod_bulk_load_gff3.pl  --gfffile GU207834.gbk.gff
> --organism 'Rabies virus' --dbname four_viruses --dbuser zc --dbpass
> 123456 --dbhost localhost --dbport 5432 --recreate_cache --noexon
> =======================================================================
>
> The url is  following:
>
> http://192.168.30.213/cgi-bin/gb2/gbrowse/four_viruses1/?name=GU207834
> =======================================================================
>
>  Thank you very much !
>
>
> **********************************************************************************
>
> On Tue, 2010-06-08 at 21:51 -0400, Scott Cain wrote:
>> Hi Zhuang,
>>
>> Can you send the full configuration file that you are using with
>> Chado?  I'm wondering if one of your track configurations has a
>> problem.
>>
>> Scott
>>
>>
>> On Tue, Jun 8, 2010 at 9:44 PM, zhuang chao <[hidden email]> wrote:
>> > hi  Scott ,
>> >
>> > I updated Bio::DB::Das::Chado to 0.26 and  added
>> >
>> > '-inferCDS 1' option to the  db_args of the  Gbrowse 2 .
>> >
>> > I  loaded  Chado with  the --noexon flag with the gff3 loader .
>> >
>> > But the question still exist. I think that may be a bug of
>> >
>> > Gbrowse 2 .
>> >
>> >
>> > ===============================================================================
>> >
>> > [Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined
>> >  value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
>> >
>> > [Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
>> >
>> >
>> > ================================================================================
>> >
>> >
>> > could  you give me a help ?  Thank you very much !
>> >
>> >
>> >
>> >
>> > On Tue, 2010-06-08 at 09:45 -0400, Scott Cain wrote:
>> >> Hi Zhuang,
>> >>
>> >> First, make sure that you have the most recent version of
>> >> Bio::DB::Das::Chado; it is 0.26.
>> >>
>> >> Next, if you loaded Chado with the --noexon flag with the gff3 loader,
>> >> you need the '-inferCDS 1' option added to you db_args.  See `perldoc
>> >> Bio::DB::Das::Chado` for more information on that and other
>> >> constructor options.
>> >>
>> >> Scott
>> >>
>> >>
>> >> 2010/6/8 zhuangchao <[hidden email]>:
>> >> > Greeting ,
>> >> >
>> >> > I have my Gbrowse 2.0 attached to a chado postgres database .
>> >> >
>> >> > Apache fails to load and give the following error in the error.log :
>> >> >
>> >> > ===============================================================================
>> >> >
>> >> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined value
>> >> > at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
>> >> >
>> >> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
>> >> >
>> >> > ================================================================================
>> >> >
>> >> > How can I solve the problem. could  you give me a help ?  Thank you very much !
>> >> >
>> >> > here is my database settings :
>> >> >
>> >> > **********************************************
>> >> >
>> >> > [four_viruses:database]
>> >> > db_adaptor    = Bio::DB::Das::Chado
>> >> >
>> >> > db_args       = -dsn
>> >> > dbi:Pg:dbname=four_viruses;host=192.168.30.213;port=5432
>> >> >                -user zc
>> >> >                -pass  123456
>> >> >
>> >> > **********************************************
>> >> >
>> >> > zhuangchao
>> >> >
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >
>> >
>> >
>>
>>
>>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: a question of Gbrowse 2

zhuang chao
hi, Scott,

I  remove all tracks .The configuration of GBrowse 2 is following:

==================================================================

[GENERAL]
description   = four_viruses1
database      = four_viruses

# examples to show in the introduction
examples = GU207834
           NC_001973



#################################
# database definitions
#################################

[four_viruses:database]
db_adaptor    = Bio::DB::Das::Chado

db_args       = -dsn dbi:Pg:dbname=four_viruses;host=localhost;port=5432
                -user zc
                -pass  123456
======================================================================

But  the problem still exist .  The error log of  apache is  following:

=====================================================================
[Thu Jun 10 17:01:21 2010] [error] [client 192.168.30.97] Can't call
method "length" on an undefined value
at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 319.,
referer:
http://192.168.30.213/cgi-bin/gb2/gbrowse/four_viruses1_test/?name=GU207834

[Thu Jun 10 17:01:21 2010] [error] [client 192.168.30.97] GBROWSE
NOTICE: To enable PDF generation, please enter the directory "/var/www"
and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown
www-data .inkscape .gnome2".  To turn off this message add "generate pdf
= 0" to the [GENERAL] section of your GBrowse.conf configuration file.,
referer:
http://192.168.30.213/cgi-bin/gb2/gbrowse/four_viruses1_test/?name=GU207834

======================================================================

So I think the problem is not  related to the  tracks .


Could  you give me a help ? Thank you very much !



On Wed, 2010-06-09 at 10:04 -0400, Scott Cain wrote:

> Hi Zhuang,
>
> I won't have time to do any testing on this until later, but in the
> meantime, I have a few suggestions:
>
> * Remove tracks that you aren't using.  I'm reasonably sure you virus
> data doesn't have any rRNA:sgd or long_terminal_repeat types.
>
> * Fix the CDS track.  It has gene features as the parent of your CDS
> features, but that is not the case.  The feature for your CDS track
> should be mRNA (that way, it's telling GBrowse when you want a CDS
> track that groups your CDS features on a given mRNA).
>
> Scott
>
>
> On Wed, Jun 9, 2010 at 6:15 AM, zhuang chao <[hidden email]> wrote:
> > hi, Scott,
> >
> > I am using the GBrowse 2.08  attached to a chado postgres database .
> >
> > The full configuration file  is in the attachment.
> >
> > The   genbank and  gff3  file   is  in  the  attachment  ,too.
> >
> > The command line of loading  gff3 file is following :
> > =======================================================================
> > perl /usr/local/bin/gmod_bulk_load_gff3.pl  --gfffile GU207834.gbk.gff
> > --organism 'Rabies virus' --dbname four_viruses --dbuser zc --dbpass
> > 123456 --dbhost localhost --dbport 5432 --recreate_cache --noexon
> > =======================================================================
> >
> > The url is  following:
> >
> > http://192.168.30.213/cgi-bin/gb2/gbrowse/four_viruses1/?name=GU207834
> > =======================================================================
> >
> >  Thank you very much !
> >
> >
> > **********************************************************************************
> >
> > On Tue, 2010-06-08 at 21:51 -0400, Scott Cain wrote:
> >> Hi Zhuang,
> >>
> >> Can you send the full configuration file that you are using with
> >> Chado?  I'm wondering if one of your track configurations has a
> >> problem.
> >>
> >> Scott
> >>
> >>
> >> On Tue, Jun 8, 2010 at 9:44 PM, zhuang chao <[hidden email]> wrote:
> >> > hi  Scott ,
> >> >
> >> > I updated Bio::DB::Das::Chado to 0.26 and  added
> >> >
> >> > '-inferCDS 1' option to the  db_args of the  Gbrowse 2 .
> >> >
> >> > I  loaded  Chado with  the --noexon flag with the gff3 loader .
> >> >
> >> > But the question still exist. I think that may be a bug of
> >> >
> >> > Gbrowse 2 .
> >> >
> >> >
> >> > ===============================================================================
> >> >
> >> > [Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined
> >> >  value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
> >> >
> >> > [Wed Jun 09 09:24:48 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
> >> >
> >> >
> >> > ================================================================================
> >> >
> >> >
> >> > could  you give me a help ?  Thank you very much !
> >> >
> >> >
> >> >
> >> >
> >> > On Tue, 2010-06-08 at 09:45 -0400, Scott Cain wrote:
> >> >> Hi Zhuang,
> >> >>
> >> >> First, make sure that you have the most recent version of
> >> >> Bio::DB::Das::Chado; it is 0.26.
> >> >>
> >> >> Next, if you loaded Chado with the --noexon flag with the gff3 loader,
> >> >> you need the '-inferCDS 1' option added to you db_args.  See `perldoc
> >> >> Bio::DB::Das::Chado` for more information on that and other
> >> >> constructor options.
> >> >>
> >> >> Scott
> >> >>
> >> >>
> >> >> 2010/6/8 zhuangchao <[hidden email]>:
> >> >> > Greeting ,
> >> >> >
> >> >> > I have my Gbrowse 2.0 attached to a chado postgres database .
> >> >> >
> >> >> > Apache fails to load and give the following error in the error.log :
> >> >> >
> >> >> > ===============================================================================
> >> >> >
> >> >> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Can't call method "length" on an undefined value
> >> >> > at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 311.
> >> >> >
> >> >> > [Tue Jun 08 03:09:13 2010] [error] [client 192.168.30.97] Premature end of script headers: gbrowse
> >> >> >
> >> >> > ================================================================================
> >> >> >
> >> >> > How can I solve the problem. could  you give me a help ?  Thank you very much !
> >> >> >
> >> >> > here is my database settings :
> >> >> >
> >> >> > **********************************************
> >> >> >
> >> >> > [four_viruses:database]
> >> >> > db_adaptor    = Bio::DB::Das::Chado
> >> >> >
> >> >> > db_args       = -dsn
> >> >> > dbi:Pg:dbname=four_viruses;host=192.168.30.213;port=5432
> >> >> >                -user zc
> >> >> >                -pass  123456
> >> >> >
> >> >> > **********************************************
> >> >> >
> >> >> > zhuangchao
> >> >> >
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >
> >> >
> >> >
> >>
> >>
> >>
> >
>
>
>



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a question of Gbrowse 2.08

zhuang chao
In reply to this post by Scott Cain
Greeting ,

I have my GBrowse 2.08 attached to a chado postgres database .

The url is  following:

http://192.168.30.94/cgi-bin/gb2/gbrowse/Baculoviruses/?name=NP_037882

Apache fails to load and give the following error in the error.log :

===============================================================================

[Mon Jun 21 09:21:49 2010] [error] [client 192.168.30.97] Can't call
method "length" on an undefined value
at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 319.

[Mon Jun 21 09:21:49 2010] [error] [client 192.168.30.97] GBROWSE
NOTICE: To enable PDF generation, please enter the directory "/var/www"
and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown
www-data .inkscape .gnome2".  To turn off this message add "generate pdf
= 0" to the [GENERAL] section of your GBrowse.conf configuration file.

[Mon Jun 21 09:21:49 2010] [error] [client 192.168.30.97] Use of
uninitialized value in concatenation (.) or string
at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render/HTML.pm line
146.

================================================================================

How can I solve the problem. could  you give me a help ?  Thank you very
much !

The full configuration file  of GBrowse 2.08 is in the attachment.  

The   genbank and  gff3  file   is  in  the  attachment  ,too.

The command line of loading  gff3 file is following :

================================================================================
perl /usr/local/bin/gmod_bulk_load_gff3.pl  --gfffile NP_037882.gbk.gff
--organism 'Spodoptera exigua MNPV' --dbname baculodb --dbuser zc
--dbpass 123456 --dbhost localhost --dbport 5432 --recreate_cache
--noexon
================================================================================



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baculodb.conf (3K) Download Attachment
GBrowse.conf (6K) Download Attachment
NP_037882.gbk (2K) Download Attachment
NP_037882.gbk.gff (991 bytes) Download Attachment
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Re: a question of Gbrowse 2.08

Scott Cain
Hi Zhang,

The GFF file you sent contains a non-standard gene representation: it
is neither gene->mRNA->CDS,UTR nor gene->mRNA->exon,polypeptide, so
the loader is going to put the features in exactly as they appear in
the GFF file.  That means that neither the --noexon loading option,
nor the -inferCDS data adaptor option will have any effect.  I am
reasonably sure the error message about "Can't call method length..."
is related to the fact that you have -inferCDS on, but the data
adaptor doesn't have any exons to infer the CDS from.

I have a few general suggestions and comments:

* When debugging GBrowse conf files, trim out any track definitions
that aren't being used.  There are only polypeptide and CDS features
in this data set, so that is all you'll be able to display in GBrowse.

* GBrowse can display things in amino acid residue coordinates, but
this configuration file isn't set up to do that, so it's going to
think this is nucleotide space.

* I don't know if the genbank2gff3 script is really geared towards
protein records.  While this GFF file was stored as written in Chado,
the usage of the CDS type on a polypeptide region is different from
how CDS types are used in Chado and GBrowse: in GBrowse, a CDS feature
is always relative to a nucleotide sequence.  Certainly, the cds glyph
in GBrowse won't work with this CDS type.  I think that this data
really ought to be represented as a single polypeptide feature rather
than as the three lines present in this file.

Scott




On Sun, Jun 20, 2010 at 9:51 PM, zhuang chao <[hidden email]> wrote:

> Greeting ,
>
> I have my GBrowse 2.08 attached to a chado postgres database .
>
> The url is  following:
>
> http://192.168.30.94/cgi-bin/gb2/gbrowse/Baculoviruses/?name=NP_037882
>
> Apache fails to load and give the following error in the error.log :
>
> ===============================================================================
>
> [Mon Jun 21 09:21:49 2010] [error] [client 192.168.30.97] Can't call
> method "length" on an undefined value
> at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 319.
>
> [Mon Jun 21 09:21:49 2010] [error] [client 192.168.30.97] GBROWSE
> NOTICE: To enable PDF generation, please enter the directory "/var/www"
> and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown
> www-data .inkscape .gnome2".  To turn off this message add "generate pdf
> = 0" to the [GENERAL] section of your GBrowse.conf configuration file.
>
> [Mon Jun 21 09:21:49 2010] [error] [client 192.168.30.97] Use of
> uninitialized value in concatenation (.) or string
> at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render/HTML.pm line
> 146.
>
> ================================================================================
>
> How can I solve the problem. could  you give me a help ?  Thank you very
> much !
>
> The full configuration file  of GBrowse 2.08 is in the attachment.
>
> The   genbank and  gff3  file   is  in  the  attachment  ,too.
>
> The command line of loading  gff3 file is following :
>
> ================================================================================
> perl /usr/local/bin/gmod_bulk_load_gff3.pl  --gfffile NP_037882.gbk.gff
> --organism 'Spodoptera exigua MNPV' --dbname baculodb --dbuser zc
> --dbpass 123456 --dbhost localhost --dbport 5432 --recreate_cache
> --noexon
> ================================================================================
>
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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