error in custom track .gff uploading

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error in custom track .gff uploading

Meenu

Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


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Fwd: error in custom track .gff uploading

Meenu


Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
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Re: error in custom track .gff uploading

Scott Cain
In reply to this post by Meenu
Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott


On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:

Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Fwd: error in custom track .gff uploading

Meenu
Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line



---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Mon, Mar 25, 2013 at 5:08 PM
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
To: Meenu Chopra <[hidden email]>
Cc: [hidden email]


Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott


On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:

Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




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



--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
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Compete for recognition, cash, and the chance to get your game
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Fwd: error in custom track .gff uploading

Meenu
Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am giving you sample file for sheep gff and conf file and few lines of and Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.



---------- Forwarded message ----------
From: Meenu Chopra <[hidden email]>
Date: Tue, Mar 26, 2013 at 5:33 AM
Subject: Fwd: [Gmod-gbrowse] error in custom track .gff uploading
To: [hidden email]


Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line



---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Mon, Mar 25, 2013 at 5:08 PM
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
To: Meenu Chopra <[hidden email]>
Cc: [hidden email]


Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott


On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:

Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




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



--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
_______________________________________________
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Re: Fwd: error in custom track .gff uploading

Scott Cain
Hi Meenu,

So did you try what I said: you can't upload the chromosome as you have in this gff file--you must have the at least the chromosomes already available with a configuration file that specifies where to find the chromosomes (ie, what database or file they are in).  Then you can upload annotations in GFF files that have those chromosomes as reference sequences.

If you want to be able to create a GBrowse instance "from scratch" (ie, uploading everything including the chromosomes), you'd have to install WebGBrowse, which is a bit more work than installing just GBrowse.  Alternatively, you could also just use the WebGBrowse instance that is running at Indiana University:

  http://webgbrowse.cgb.indiana.edu/cgi-bin/webgbrowse/uploadData

Scott


On Tue, Mar 26, 2013 at 1:43 AM, Meenu Chopra <[hidden email]> wrote:
Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am giving you sample file for sheep gff and conf file and few lines of and Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.



---------- Forwarded message ----------
From: Meenu Chopra <[hidden email]>
Date: Tue, Mar 26, 2013 at 5:33 AM
Subject: Fwd: [Gmod-gbrowse] error in custom track .gff uploading
To: [hidden email]


Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line



---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Mon, Mar 25, 2013 at 5:08 PM
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
To: Meenu Chopra <[hidden email]>
Cc: [hidden email]


Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott


On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:

Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
_______________________________________________
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------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
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Re: Fwd: error in custom track .gff uploading

Jayaraman, Pushkala
In reply to this post by Meenu

I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.

 

Pushkala

 

From: Meenu Chopra [mailto:[hidden email]]
Sent: Tuesday, March 26, 2013 12:33 AM
To: [hidden email]
Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line


---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Mon, Mar 25, 2013 at 5:08 PM
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
To: Meenu Chopra <[hidden email]>
Cc: [hidden email]


Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott

On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:


Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal

 

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
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Re: Fwd: error in custom track .gff uploading

Scott Cain
Thanks for reminding me Pushkala: I meant to as what this was all about:

  database = database_0 # do not change this!

In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.

Scott


On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.

 

Pushkala

 

From: Meenu Chopra [mailto:[hidden email]]
Sent: Tuesday, March 26, 2013 12:33 AM
To: [hidden email]
Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line


---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Mon, Mar 25, 2013 at 5:08 PM
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
To: Meenu Chopra <[hidden email]>
Cc: [hidden email]


Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott

On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:


Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal

 

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
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Re: Fwd: error in custom track .gff uploading

Meenu
HiiI Scott , Pushkala

I have  tried , what u suggest me,

I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.

Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.

I am sending You .conf file created by me but not showing any annotation.

please help me out.

Thanks




On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:
Thanks for reminding me Pushkala: I meant to as what this was all about:

  database = database_0 # do not change this!

In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.

Scott


On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.

 

Pushkala

 

From: Meenu Chopra [mailto:[hidden email]]
Sent: Tuesday, March 26, 2013 12:33 AM
To: [hidden email]
Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line


---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Mon, Mar 25, 2013 at 5:08 PM
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
To: Meenu Chopra <[hidden email]>
Cc: [hidden email]


Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott

On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:


Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal

 

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




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



--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
_______________________________________________
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sheep.conf (3K) Download Attachment
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Re: Fwd: error in custom track .gff uploading

Scott Cain
Hi Meenu,

Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.

So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?

When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?

Scott




On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:
HiiI Scott , Pushkala

I have  tried , what u suggest me,

I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.

Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.

I am sending You .conf file created by me but not showing any annotation.

please help me out.

Thanks




On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:
Thanks for reminding me Pushkala: I meant to as what this was all about:

  database = database_0 # do not change this!

In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.

Scott


On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.

 

Pushkala

 

From: Meenu Chopra [mailto:[hidden email]]
Sent: Tuesday, March 26, 2013 12:33 AM
To: [hidden email]
Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line


---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Mon, Mar 25, 2013 at 5:08 PM
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
To: Meenu Chopra <[hidden email]>
Cc: [hidden email]


Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott

On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:


Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal

 

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
_______________________________________________
Gmod-gbrowse mailing list
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Re: Fwd: error in custom track .gff uploading

Jayaraman, Pushkala

Why do you have this “###”  in the middle in your Gff3 file?

 

chrUn_GL339607              UCSC     chromosome     1              215         .               .               .                Name=chrUn_GL339607;ID=chrUn_GL339607

chrUn_GL339884              UCSC     chromosome     1              195         .               .               .                Name=chrUn_GL339884;ID=chrUn_GL339884

chrUn_GL340145              UCSC     chromosome     1              47           .               .               .                Name=chrUn_GL340145;ID=chrUn_GL340145

###

chr1       refGene               gene      2625494                2628369                .               -              .                Name=PRLH;ID=PRLH;status=Provisional

chr1       refGene               mRNA   2625494                2628369                .               -              .                Name=NM_001009434;Parent=PRLH;ID=NM_001009434;Alias=PRLH;status=Provisional

chr1       refGene               exon      2625494                2625786                .               -              .                Name=NM_001009434.exon2;Parent=NM_001009434;ID=NM_001009434.exon2

 

I just uploaded a part of your Gff3 file (just Chr1) onto my browser to see if it pulls up data and it does..

So it looks like a part of Gff3 file is fine.. check what those “###” patterns are doing in your file..

 

 

Pushkala

 

 

From: Scott Cain [mailto:[hidden email]]
Sent: Monday, April 01, 2013 10:19 AM
To: Meenu Chopra
Cc: Jayaraman, Pushkala; [hidden email]
Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

Hi Meenu,

Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.

So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?

When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?

Scott



On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:

HiiI Scott , Pushkala

I have  tried , what u suggest me,

I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.

Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.

I am sending You .conf file created by me but not showing any annotation.

please help me out.

Thanks

 

 

 

On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:

Thanks for reminding me Pushkala: I meant to as what this was all about:

  database = database_0 # do not change this!

In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.

Scott

On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.

 

Pushkala

 

From: Meenu Chopra [mailto:[hidden email]]
Sent: Tuesday, March 26, 2013 12:33 AM
To: [hidden email]
Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line

---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Mon, Mar 25, 2013 at 5:08 PM
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
To: Meenu Chopra <[hidden email]>
Cc: [hidden email]


Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott

On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:


Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal

 

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal

 

------------------------------------------------------------------------------
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Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal




--
------------------------------------------------------------------------
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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Compete for recognition, cash, and the chance to get your game
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Re: Fwd: error in custom track .gff uploading

Scott Cain
The ### directive is part of the GFF3 spec--it indicates that all Parent-child relationships up to that point have been resolved.  If that is leading to a problem then there is a bug related to GFF parsing.

Scott



On Mon, Apr 1, 2013 at 6:21 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Why do you have this “###”  in the middle in your Gff3 file?

 

chrUn_GL339607              UCSC     chromosome     1              215         .               .               .                Name=chrUn_GL339607;ID=chrUn_GL339607

chrUn_GL339884              UCSC     chromosome     1              195         .               .               .                Name=chrUn_GL339884;ID=chrUn_GL339884

chrUn_GL340145              UCSC     chromosome     1              47           .               .               .                Name=chrUn_GL340145;ID=chrUn_GL340145

###

chr1       refGene               gene      2625494                2628369                .               -              .                Name=PRLH;ID=PRLH;status=Provisional

chr1       refGene               mRNA   2625494                2628369                .               -              .                Name=NM_001009434;Parent=PRLH;ID=NM_001009434;Alias=PRLH;status=Provisional

chr1       refGene               exon      2625494                2625786                .               -              .                Name=NM_001009434.exon2;Parent=NM_001009434;ID=NM_001009434.exon2

 

I just uploaded a part of your Gff3 file (just Chr1) onto my browser to see if it pulls up data and it does..

So it looks like a part of Gff3 file is fine.. check what those “###” patterns are doing in your file..

 

 

Pushkala

 

 

From: Scott Cain [mailto:[hidden email]]
Sent: Monday, April 01, 2013 10:19 AM
To: Meenu Chopra
Cc: Jayaraman, Pushkala; [hidden email]
Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

Hi Meenu,

Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.

So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?

When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?

Scott



On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:

HiiI Scott , Pushkala

I have  tried , what u suggest me,

I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.

Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.

I am sending You .conf file created by me but not showing any annotation.

please help me out.

Thanks

 

 

 

On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:

Thanks for reminding me Pushkala: I meant to as what this was all about:

  database = database_0 # do not change this!

In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.

Scott

On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.

 

Pushkala

 

From: Meenu Chopra [mailto:[hidden email]]
Sent: Tuesday, March 26, 2013 12:33 AM
To: [hidden email]
Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line

---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Mon, Mar 25, 2013 at 5:08 PM
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
To: Meenu Chopra <[hidden email]>
Cc: [hidden email]


Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott

On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:


Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal

 

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal

 

------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




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

------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
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Re: error in custom track .gff uploading

Fields, Christopher J
In reply to this post by Jayaraman, Pushkala
Pushkala,

'###' is valid GFF3 and actually has a use (from the GFF3 spec):

-----------------------------------------
This directive (three # signs in a row) indicates that all forward references to feature IDs that have been seen to this point have been resolved. After seeing this directive, a program that is processing the file serially can close off any open objects that it has created and return them, thereby allowing iterative access to the file. Otherwise, software cannot know that a feature has been fully populated by its subfeatures until the end of the file has been reached. It is recommended that complex features, such as the canonical gene, be terminated with the ### notation.
-----------------------------------------

chris

On Apr 1, 2013, at 5:21 PM, "Jayaraman, Pushkala" <[hidden email]> wrote:

> Why do you have this “###”  in the middle in your Gff3 file?
>  
> chrUn_GL339607              UCSC     chromosome     1              215         .               .               .                Name=chrUn_GL339607;ID=chrUn_GL339607
> chrUn_GL339884              UCSC     chromosome     1              195         .               .               .                Name=chrUn_GL339884;ID=chrUn_GL339884
> chrUn_GL340145              UCSC     chromosome     1              47           .               .               .                Name=chrUn_GL340145;ID=chrUn_GL340145
> ###
> chr1       refGene               gene      2625494                2628369                .               -              .                Name=PRLH;ID=PRLH;status=Provisional
> chr1       refGene               mRNA   2625494                2628369                .               -              .                Name=NM_001009434;Parent=PRLH;ID=NM_001009434;Alias=PRLH;status=Provisional
> chr1       refGene               exon      2625494                2625786                .               -              .                Name=NM_001009434.exon2;Parent=NM_001009434;ID=NM_001009434.exon2
>  
> I just uploaded a part of your Gff3 file (just Chr1) onto my browser to see if it pulls up data and it does..
> So it looks like a part of Gff3 file is fine.. check what those “###” patterns are doing in your file..
>  
> <image001.jpg>
>  
> Pushkala
>  
>  
> From: Scott Cain [mailto:[hidden email]]
> Sent: Monday, April 01, 2013 10:19 AM
> To: Meenu Chopra
> Cc: Jayaraman, Pushkala; [hidden email]
> Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>  
> Hi Meenu,
>
> Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.
>
> So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?
>
> When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?
>
> Scott
>
>
>
>
> On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:
> HiiI Scott , Pushkala
>
> I have  tried , what u suggest me,
>
> I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.
>
> Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.
>
> I am sending You .conf file created by me but not showing any annotation.
>
> please help me out.
>
> Thanks
>  
>  
>  
>
> On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:
> Thanks for reminding me Pushkala: I meant to as what this was all about:
>
>   database = database_0 # do not change this!
>
> In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.
>
> Scott
>
>
> On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:
> I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.
>  
> Pushkala
>  
> From: Meenu Chopra [mailto:[hidden email]]
> Sent: Tuesday, March 26, 2013 12:33 AM
> To: [hidden email]
> Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>  
> Hii Scott
>
> You are absolutely right, i have the same problem what you are getting.
>
> I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.
>
> Error msg:
>
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line
>
>
> ---------- Forwarded message ----------
> From: Scott Cain <[hidden email]>
> Date: Mon, Mar 25, 2013 at 5:08 PM
> Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
> To: Meenu Chopra <[hidden email]>
> Cc: [hidden email]
>
>
> Hi Meenu,
>
> Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?).  
>
> Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?
>
> If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.
>
> Does your apache error log have any error messages in it that might point to the problem?
>
> Scott
>
> On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:
>
> Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.
>
> In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )
>
> I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.
>
> Please check it out once, and let me know is there any problem in .conf file or something else.
>
> Thanks
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>  
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>  
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
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> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d_______________________________________________
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Compete for recognition, cash, and the chance to get your game
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Re: Fwd: error in custom track .gff uploading

Jayaraman, Pushkala
In reply to this post by Scott Cain

Oops! My bad! J

Please discard my earlier email..

But yes.. the Gff3 file does load successfully from the custom URL loader and does display successfully…

 

Pushkala

 

From: Scott Cain [mailto:[hidden email]]
Sent: Monday, April 01, 2013 5:24 PM
To: Jayaraman, Pushkala
Cc: Meenu Chopra; [hidden email]
Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

The ### directive is part of the GFF3 spec--it indicates that all Parent-child relationships up to that point have been resolved.  If that is leading to a problem then there is a bug related to GFF parsing.

Scott

 

On Mon, Apr 1, 2013 at 6:21 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Why do you have this “###”  in the middle in your Gff3 file?

 

chrUn_GL339607              UCSC     chromosome     1              215         .               .               .                Name=chrUn_GL339607;ID=chrUn_GL339607

chrUn_GL339884              UCSC     chromosome     1              195         .               .               .                Name=chrUn_GL339884;ID=chrUn_GL339884

chrUn_GL340145              UCSC     chromosome     1              47           .               .               .                Name=chrUn_GL340145;ID=chrUn_GL340145

###

chr1       refGene               gene      2625494                2628369                .               -              .                Name=PRLH;ID=PRLH;status=Provisional

chr1       refGene               mRNA   2625494                2628369                .               -              .                Name=NM_001009434;Parent=PRLH;ID=NM_001009434;Alias=PRLH;status=Provisional

chr1       refGene               exon      2625494                2625786                .               -              .                Name=NM_001009434.exon2;Parent=NM_001009434;ID=NM_001009434.exon2

 

I just uploaded a part of your Gff3 file (just Chr1) onto my browser to see if it pulls up data and it does..

So it looks like a part of Gff3 file is fine.. check what those “###” patterns are doing in your file..

 

 

Pushkala

 

 

From: Scott Cain [mailto:[hidden email]]
Sent: Monday, April 01, 2013 10:19 AM
To: Meenu Chopra
Cc: Jayaraman, Pushkala; [hidden email]
Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

Hi Meenu,

Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.

So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?

When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?

Scott


On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:

HiiI Scott , Pushkala

I have  tried , what u suggest me,

I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.

Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.

I am sending You .conf file created by me but not showing any annotation.

please help me out.

Thanks

 

 

 

On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:

Thanks for reminding me Pushkala: I meant to as what this was all about:

  database = database_0 # do not change this!

In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.

Scott

On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.

 

Pushkala

 

From: Meenu Chopra [mailto:[hidden email]]
Sent: Tuesday, March 26, 2013 12:33 AM
To: [hidden email]
Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading

 

Hii Scott

You are absolutely right, i have the same problem what you are getting.

I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.

Error msg:

Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line

---------- Forwarded message ----------
From: Scott Cain <[hidden email]>
Date: Mon, Mar 25, 2013 at 5:08 PM
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
To: Meenu Chopra <[hidden email]>
Cc: [hidden email]


Hi Meenu,

Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?). 

Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?

If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.

Does your apache error log have any error messages in it that might point to the problem?

Scott

On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:


Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.

In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )

I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.

Please check it out once, and let me know is there any problem in .conf file or something else.

Thanks
--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal

 

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal

 

------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d

_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




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


------------------------------------------------------------------------------
Own the Future-Intel&reg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
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Re: error in custom track .gff uploading

Meenu
In reply to this post by Fields, Christopher J
Hii Scott

For uploading only sheep .gff file I have used bp_seqfeature_load.pl command for uploading the .gff file into database, its not giving any error ( attached screen shot) .
And its running fine on browser also, apache error log does not contain any error msg, its only giving warning msg.

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet


Problem is only when I am uploading sheep file in custom track with cattle browser page, at the time of uploading sheep .gff its showing msg in error.log file.

Error msg:

No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.
No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.

1000 features processed
[4172] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
2000 features processed
3000 features processed
4000 features processed
5000 features processed
6000 features processed
7000 features processed
8000 features processed
9000 features processed
10000 features processed
11000 features processed
[4174] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
12000 features processed
13000 features processed

Any suggestion will be appreciable.

Thanks


On Mon, Apr 1, 2013 at 11:28 PM, Fields, Christopher J <[hidden email]> wrote:
Pushkala,

'###' is valid GFF3 and actually has a use (from the GFF3 spec):

-----------------------------------------
This directive (three # signs in a row) indicates that all forward references to feature IDs that have been seen to this point have been resolved. After seeing this directive, a program that is processing the file serially can close off any open objects that it has created and return them, thereby allowing iterative access to the file. Otherwise, software cannot know that a feature has been fully populated by its subfeatures until the end of the file has been reached. It is recommended that complex features, such as the canonical gene, be terminated with the ### notation.
-----------------------------------------

chris

On Apr 1, 2013, at 5:21 PM, "Jayaraman, Pushkala" <[hidden email]> wrote:

> Why do you have this “###”  in the middle in your Gff3 file?
>
> chrUn_GL339607              UCSC     chromosome     1              215         .               .               .                Name=chrUn_GL339607;ID=chrUn_GL339607
> chrUn_GL339884              UCSC     chromosome     1              195         .               .               .                Name=chrUn_GL339884;ID=chrUn_GL339884
> chrUn_GL340145              UCSC     chromosome     1              47           .               .               .                Name=chrUn_GL340145;ID=chrUn_GL340145
> ###
> chr1       refGene               gene      2625494                2628369                .               -              .                Name=PRLH;ID=PRLH;status=Provisional
> chr1       refGene               mRNA   2625494                2628369                .               -              .                Name=NM_001009434;Parent=PRLH;ID=NM_001009434;Alias=PRLH;status=Provisional
> chr1       refGene               exon      2625494                2625786                .               -              .                Name=NM_001009434.exon2;Parent=NM_001009434;ID=NM_001009434.exon2
>
> I just uploaded a part of your Gff3 file (just Chr1) onto my browser to see if it pulls up data and it does..
> So it looks like a part of Gff3 file is fine.. check what those “###” patterns are doing in your file..
>
> <image001.jpg>
>
> Pushkala
>
>
> From: Scott Cain [mailto:[hidden email]]
> Sent: Monday, April 01, 2013 10:19 AM
> To: Meenu Chopra
> Cc: Jayaraman, Pushkala; [hidden email]
> Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hi Meenu,
>
> Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.
>
> So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?
>
> When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?
>
> Scott
>
>
>
>
> On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:
> HiiI Scott , Pushkala
>
> I have  tried , what u suggest me,
>
> I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.
>
> Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.
>
> I am sending You .conf file created by me but not showing any annotation.
>
> please help me out.
>
> Thanks
>
>
>
>
> On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:
> Thanks for reminding me Pushkala: I meant to as what this was all about:
>
>   database = database_0 # do not change this!
>
> In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.
>
> Scott
>
>
> On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:
> I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.
>
> Pushkala
>
> From: Meenu Chopra [mailto:[hidden email]]
> Sent: Tuesday, March 26, 2013 12:33 AM
> To: [hidden email]
> Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hii Scott
>
> You are absolutely right, i have the same problem what you are getting.
>
> I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.
>
> Error msg:
>
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line
>
>
> ---------- Forwarded message ----------
> From: Scott Cain <[hidden email]>
> Date: Mon, Mar 25, 2013 at 5:08 PM
> Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
> To: Meenu Chopra <[hidden email]>
> Cc: [hidden email]
>
>
> Hi Meenu,
>
> Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?).
>
> Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?
>
> If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.
>
> Does your apache error log have any error messages in it that might point to the problem?
>
> Scott
>
> On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:
>
> Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.
>
> In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )
>
> I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.
>
> Please check it out once, and let me know is there any problem in .conf file or something else.
>
> Thanks
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
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Re: error in custom track .gff uploading

Meenu
Hii Pushkala

Did u make any database for uploading that gff file or made any changes in .conf file which is generated by default.
Because I also tried to upload only chr 1 gff file,  still its not showing any annotation.
Can you Please send me that .gff and .conf file which you uploaded into custom track.

Thanks


On Tue, Apr 2, 2013 at 9:35 AM, Meenu Chopra <[hidden email]> wrote:
Hii Scott

For uploading only sheep .gff file I have used bp_seqfeature_load.pl command for uploading the .gff file into database, its not giving any error ( attached screen shot) .
And its running fine on browser also, apache error log does not contain any error msg, its only giving warning msg.

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet


Problem is only when I am uploading sheep file in custom track with cattle browser page, at the time of uploading sheep .gff its showing msg in error.log file.

Error msg:

No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.
No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.

1000 features processed
[4172] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
2000 features processed
3000 features processed
4000 features processed
5000 features processed
6000 features processed
7000 features processed
8000 features processed
9000 features processed
10000 features processed
11000 features processed
[4174] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
12000 features processed
13000 features processed

Any suggestion will be appreciable.

Thanks



On Mon, Apr 1, 2013 at 11:28 PM, Fields, Christopher J <[hidden email]> wrote:
Pushkala,

'###' is valid GFF3 and actually has a use (from the GFF3 spec):

-----------------------------------------
This directive (three # signs in a row) indicates that all forward references to feature IDs that have been seen to this point have been resolved. After seeing this directive, a program that is processing the file serially can close off any open objects that it has created and return them, thereby allowing iterative access to the file. Otherwise, software cannot know that a feature has been fully populated by its subfeatures until the end of the file has been reached. It is recommended that complex features, such as the canonical gene, be terminated with the ### notation.
-----------------------------------------

chris

On Apr 1, 2013, at 5:21 PM, "Jayaraman, Pushkala" <[hidden email]> wrote:

> Why do you have this “###”  in the middle in your Gff3 file?
>
> chrUn_GL339607              UCSC     chromosome     1              215         .               .               .                Name=chrUn_GL339607;ID=chrUn_GL339607
> chrUn_GL339884              UCSC     chromosome     1              195         .               .               .                Name=chrUn_GL339884;ID=chrUn_GL339884
> chrUn_GL340145              UCSC     chromosome     1              47           .               .               .                Name=chrUn_GL340145;ID=chrUn_GL340145
> ###
> chr1       refGene               gene      2625494                2628369                .               -              .                Name=PRLH;ID=PRLH;status=Provisional
> chr1       refGene               mRNA   2625494                2628369                .               -              .                Name=NM_001009434;Parent=PRLH;ID=NM_001009434;Alias=PRLH;status=Provisional
> chr1       refGene               exon      2625494                2625786                .               -              .                Name=NM_001009434.exon2;Parent=NM_001009434;ID=NM_001009434.exon2
>
> I just uploaded a part of your Gff3 file (just Chr1) onto my browser to see if it pulls up data and it does..
> So it looks like a part of Gff3 file is fine.. check what those “###” patterns are doing in your file..
>
> <image001.jpg>
>
> Pushkala
>
>
> From: Scott Cain [mailto:[hidden email]]
> Sent: Monday, April 01, 2013 10:19 AM
> To: Meenu Chopra
> Cc: Jayaraman, Pushkala; [hidden email]
> Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hi Meenu,
>
> Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.
>
> So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?
>
> When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?
>
> Scott
>
>
>
>
> On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:
> HiiI Scott , Pushkala
>
> I have  tried , what u suggest me,
>
> I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.
>
> Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.
>
> I am sending You .conf file created by me but not showing any annotation.
>
> please help me out.
>
> Thanks
>
>
>
>
> On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:
> Thanks for reminding me Pushkala: I meant to as what this was all about:
>
>   database = database_0 # do not change this!
>
> In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.
>
> Scott
>
>
> On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:
> I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.
>
> Pushkala
>
> From: Meenu Chopra [mailto:[hidden email]]
> Sent: Tuesday, March 26, 2013 12:33 AM
> To: [hidden email]
> Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hii Scott
>
> You are absolutely right, i have the same problem what you are getting.
>
> I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.
>
> Error msg:
>
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line
>
>
> ---------- Forwarded message ----------
> From: Scott Cain <[hidden email]>
> Date: Mon, Mar 25, 2013 at 5:08 PM
> Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
> To: Meenu Chopra <[hidden email]>
> Cc: [hidden email]
>
>
> Hi Meenu,
>
> Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?).
>
> Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?
>
> If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.
>
> Does your apache error log have any error messages in it that might point to the problem?
>
> Scott
>
> On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:
>
> Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.
>
> In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )
>
> I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.
>
> Please check it out once, and let me know is there any problem in .conf file or something else.
>
> Thanks
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
_______________________________________________
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Re: error in custom track .gff uploading

Scott Cain
Meenu,

There is a message about "no upload_db_adaptor set in GBrowse.conf..." and that it is trying to use DBD::SQLite.  Do you have DBD::SQLite installed?  If not, it certainly isn't going to work since that is what it is trying to use.  You could also change the configuration to use MySQL or just use files in the files system (this is the "memory" option, the slowest of the available options).  Please see the comments in the GBrowse.conf file for guidance, as well as the documentation at http://gmod.org/wiki/GBrowse_User_Uploads.

Scott



On Tue, Apr 2, 2013 at 4:40 AM, Meenu Chopra <[hidden email]> wrote:
Hii Pushkala

Did u make any database for uploading that gff file or made any changes in .conf file which is generated by default.
Because I also tried to upload only chr 1 gff file,  still its not showing any annotation.
Can you Please send me that .gff and .conf file which you uploaded into custom track.

Thanks


On Tue, Apr 2, 2013 at 9:35 AM, Meenu Chopra <[hidden email]> wrote:
Hii Scott

For uploading only sheep .gff file I have used bp_seqfeature_load.pl command for uploading the .gff file into database, its not giving any error ( attached screen shot) .
And its running fine on browser also, apache error log does not contain any error msg, its only giving warning msg.

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet


Problem is only when I am uploading sheep file in custom track with cattle browser page, at the time of uploading sheep .gff its showing msg in error.log file.

Error msg:

No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.
No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.

1000 features processed
[4172] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
2000 features processed
3000 features processed
4000 features processed
5000 features processed
6000 features processed
7000 features processed
8000 features processed
9000 features processed
10000 features processed
11000 features processed
[4174] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
12000 features processed
13000 features processed

Any suggestion will be appreciable.

Thanks



On Mon, Apr 1, 2013 at 11:28 PM, Fields, Christopher J <[hidden email]> wrote:
Pushkala,

'###' is valid GFF3 and actually has a use (from the GFF3 spec):

-----------------------------------------
This directive (three # signs in a row) indicates that all forward references to feature IDs that have been seen to this point have been resolved. After seeing this directive, a program that is processing the file serially can close off any open objects that it has created and return them, thereby allowing iterative access to the file. Otherwise, software cannot know that a feature has been fully populated by its subfeatures until the end of the file has been reached. It is recommended that complex features, such as the canonical gene, be terminated with the ### notation.
-----------------------------------------

chris

On Apr 1, 2013, at 5:21 PM, "Jayaraman, Pushkala" <[hidden email]> wrote:

> Why do you have this “###”  in the middle in your Gff3 file?
>
> chrUn_GL339607              UCSC     chromosome     1              215         .               .               .                Name=chrUn_GL339607;ID=chrUn_GL339607
> chrUn_GL339884              UCSC     chromosome     1              195         .               .               .                Name=chrUn_GL339884;ID=chrUn_GL339884
> chrUn_GL340145              UCSC     chromosome     1              47           .               .               .                Name=chrUn_GL340145;ID=chrUn_GL340145
> ###
> chr1       refGene               gene      2625494                2628369                .               -              .                Name=PRLH;ID=PRLH;status=Provisional
> chr1       refGene               mRNA   2625494                2628369                .               -              .                Name=NM_001009434;Parent=PRLH;ID=NM_001009434;Alias=PRLH;status=Provisional
> chr1       refGene               exon      2625494                2625786                .               -              .                Name=NM_001009434.exon2;Parent=NM_001009434;ID=NM_001009434.exon2
>
> I just uploaded a part of your Gff3 file (just Chr1) onto my browser to see if it pulls up data and it does..
> So it looks like a part of Gff3 file is fine.. check what those “###” patterns are doing in your file..
>
> <image001.jpg>
>
> Pushkala
>
>
> From: Scott Cain [mailto:[hidden email]]
> Sent: Monday, April 01, 2013 10:19 AM
> To: Meenu Chopra
> Cc: Jayaraman, Pushkala; [hidden email]
> Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hi Meenu,
>
> Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.
>
> So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?
>
> When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?
>
> Scott
>
>
>
>
> On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:
> HiiI Scott , Pushkala
>
> I have  tried , what u suggest me,
>
> I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.
>
> Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.
>
> I am sending You .conf file created by me but not showing any annotation.
>
> please help me out.
>
> Thanks
>
>
>
>
> On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:
> Thanks for reminding me Pushkala: I meant to as what this was all about:
>
>   database = database_0 # do not change this!
>
> In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.
>
> Scott
>
>
> On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:
> I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.
>
> Pushkala
>
> From: Meenu Chopra [mailto:[hidden email]]
> Sent: Tuesday, March 26, 2013 12:33 AM
> To: [hidden email]
> Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hii Scott
>
> You are absolutely right, i have the same problem what you are getting.
>
> I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.
>
> Error msg:
>
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line
>
>
> ---------- Forwarded message ----------
> From: Scott Cain <[hidden email]>
> Date: Mon, Mar 25, 2013 at 5:08 PM
> Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
> To: Meenu Chopra <[hidden email]>
> Cc: [hidden email]
>
>
> Hi Meenu,
>
> Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?).
>
> Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?
>
> If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.
>
> Does your apache error log have any error messages in it that might point to the problem?
>
> Scott
>
> On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:
>
> Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.
>
> In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )
>
> I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.
>
> Please check it out once, and let me know is there any problem in .conf file or something else.
>
> Thanks
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
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>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
> _______________________________________________
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>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d_______________________________________________
> Gmod-gbrowse mailing list
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal




--
------------------------------------------------------------------------
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: error in custom track .gff uploading

Jayaraman, Pushkala

I agree with Scott.

You may also need to configure your Gbrowse to use either MYSQL or SQLite database to use that in your Gbrowse.conf.

I didn’t make any changes in the conf file or the gff3 file.

 

Pushkala

 

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, April 02, 2013 9:50 AM
To: Meenu Chopra
Cc: Fields, Christopher J; Jayaraman, Pushkala; [hidden email]
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading

 

Meenu,

There is a message about "no upload_db_adaptor set in GBrowse.conf..." and that it is trying to use DBD::SQLite.  Do you have DBD::SQLite installed?  If not, it certainly isn't going to work since that is what it is trying to use.  You could also change the configuration to use MySQL or just use files in the files system (this is the "memory" option, the slowest of the available options).  Please see the comments in the GBrowse.conf file for guidance, as well as the documentation at http://gmod.org/wiki/GBrowse_User_Uploads.

Scott

 

On Tue, Apr 2, 2013 at 4:40 AM, Meenu Chopra <[hidden email]> wrote:

Hii Pushkala

Did u make any database for uploading that gff file or made any changes in .conf file which is generated by default.

Because I also tried to upload only chr 1 gff file,  still its not showing any annotation.

Can you Please send me that .gff and .conf file which you uploaded into custom track.

Thanks

 

On Tue, Apr 2, 2013 at 9:35 AM, Meenu Chopra <[hidden email]> wrote:

Hii Scott

For uploading only sheep .gff file I have used bp_seqfeature_load.pl command for uploading the .gff file into database, its not giving any error ( attached screen shot) .
And its running fine on browser also, apache error log does not contain any error msg, its only giving warning msg.

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet


Problem is only when I am uploading sheep file in custom track with cattle browser page, at the time of uploading sheep .gff its showing msg in error.log file.

Error msg:


No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.
No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.

1000 features processed
[4172] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
2000 features processed
3000 features processed
4000 features processed
5000 features processed
6000 features processed
7000 features processed
8000 features processed
9000 features processed
10000 features processed
11000 features processed
[4174] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
12000 features processed
13000 features processed

Any suggestion will be appreciable.

Thanks

 

 

On Mon, Apr 1, 2013 at 11:28 PM, Fields, Christopher J <[hidden email]> wrote:

Pushkala,

'###' is valid GFF3 and actually has a use (from the GFF3 spec):

-----------------------------------------
This directive (three # signs in a row) indicates that all forward references to feature IDs that have been seen to this point have been resolved. After seeing this directive, a program that is processing the file serially can close off any open objects that it has created and return them, thereby allowing iterative access to the file. Otherwise, software cannot know that a feature has been fully populated by its subfeatures until the end of the file has been reached. It is recommended that complex features, such as the canonical gene, be terminated with the ### notation.
-----------------------------------------

chris


On Apr 1, 2013, at 5:21 PM, "Jayaraman, Pushkala" <[hidden email]> wrote:

> Why do you have this “###”  in the middle in your Gff3 file?
>
> chrUn_GL339607              UCSC     chromosome     1              215         .               .               .                Name=chrUn_GL339607;ID=chrUn_GL339607
> chrUn_GL339884              UCSC     chromosome     1              195         .               .               .                Name=chrUn_GL339884;ID=chrUn_GL339884
> chrUn_GL340145              UCSC     chromosome     1              47           .               .               .                Name=chrUn_GL340145;ID=chrUn_GL340145
> ###
> chr1       refGene               gene      2625494                2628369                .               -              .                Name=PRLH;ID=PRLH;status=Provisional
> chr1       refGene               mRNA   2625494                2628369                .               -              .                Name=NM_001009434;Parent=PRLH;ID=NM_001009434;Alias=PRLH;status=Provisional
> chr1       refGene               exon      2625494                2625786                .               -              .                Name=NM_001009434.exon2;Parent=NM_001009434;ID=NM_001009434.exon2
>
> I just uploaded a part of your Gff3 file (just Chr1) onto my browser to see if it pulls up data and it does..
> So it looks like a part of Gff3 file is fine.. check what those “###” patterns are doing in your file..
>

> <image001.jpg>

>
> Pushkala
>
>
> From: Scott Cain [mailto:[hidden email]]
> Sent: Monday, April 01, 2013 10:19 AM
> To: Meenu Chopra
> Cc: Jayaraman, Pushkala; [hidden email]
> Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hi Meenu,
>
> Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.
>
> So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?
>
> When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?
>
> Scott
>
>
>
>
> On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:
> HiiI Scott , Pushkala
>
> I have  tried , what u suggest me,
>
> I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.
>
> Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.
>
> I am sending You .conf file created by me but not showing any annotation.
>
> please help me out.
>
> Thanks
>
>
>
>
> On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:
> Thanks for reminding me Pushkala: I meant to as what this was all about:
>
>   database = database_0 # do not change this!
>
> In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.
>
> Scott
>
>
> On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:
> I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.
>
> Pushkala
>
> From: Meenu Chopra [mailto:[hidden email]]
> Sent: Tuesday, March 26, 2013 12:33 AM
> To: [hidden email]
> Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hii Scott
>
> You are absolutely right, i have the same problem what you are getting.
>
> I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.
>
> Error msg:
>
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line
>
>
> ---------- Forwarded message ----------
> From: Scott Cain <[hidden email]>
> Date: Mon, Mar 25, 2013 at 5:08 PM
> Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
> To: Meenu Chopra <[hidden email]>
> Cc: [hidden email]
>
>
> Hi Meenu,
>
> Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?).
>
> Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?
>
> If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.
>
> Does your apache error log have any error messages in it that might point to the problem?
>
> Scott
>
> On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:
>
> Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.
>
> In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )
>
> I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.
>
> Please check it out once, and let me know is there any problem in .conf file or something else.
>
> Thanks
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal




--
------------------------------------------------------------------------
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: error in custom track .gff uploading

Meenu
Hiiiii Pushkala, Scott

I have installed SQLite and make changes in gbrowse.conf file also, now  in log file its not showing error like:

No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.

its showing only

1000 features processed
[11129] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_44016 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
2000 features processed
3000 features processed
4000 features processed
5000 features processed
6000 features processed
7000 features processed
8000 features processed
9000 features processed
10000 features processed
11000 features processed
[11132] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_44016 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
12000 features processed
13000 features processed

Still its not showing any annotation on browser. I am attaching  Gbrowse.conf file.

Please look into it, and help me out.

Thanks


On Tue, Apr 2, 2013 at 10:25 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I agree with Scott.

You may also need to configure your Gbrowse to use either MYSQL or SQLite database to use that in your Gbrowse.conf.

I didn’t make any changes in the conf file or the gff3 file.

 

Pushkala

 

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, April 02, 2013 9:50 AM
To: Meenu Chopra
Cc: Fields, Christopher J; Jayaraman, Pushkala; [hidden email]
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading

 

Meenu,

There is a message about "no upload_db_adaptor set in GBrowse.conf..." and that it is trying to use DBD::SQLite.  Do you have DBD::SQLite installed?  If not, it certainly isn't going to work since that is what it is trying to use.  You could also change the configuration to use MySQL or just use files in the files system (this is the "memory" option, the slowest of the available options).  Please see the comments in the GBrowse.conf file for guidance, as well as the documentation at http://gmod.org/wiki/GBrowse_User_Uploads.

Scott

 

On Tue, Apr 2, 2013 at 4:40 AM, Meenu Chopra <[hidden email]> wrote:

Hii Pushkala

Did u make any database for uploading that gff file or made any changes in .conf file which is generated by default.

Because I also tried to upload only chr 1 gff file,  still its not showing any annotation.

Can you Please send me that .gff and .conf file which you uploaded into custom track.

Thanks

 

On Tue, Apr 2, 2013 at 9:35 AM, Meenu Chopra <[hidden email]> wrote:

Hii Scott

For uploading only sheep .gff file I have used bp_seqfeature_load.pl command for uploading the .gff file into database, its not giving any error ( attached screen shot) .
And its running fine on browser also, apache error log does not contain any error msg, its only giving warning msg.

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet


Problem is only when I am uploading sheep file in custom track with cattle browser page, at the time of uploading sheep .gff its showing msg in error.log file.

Error msg:


No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.
No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.

1000 features processed
[4172] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
2000 features processed
3000 features processed
4000 features processed
5000 features processed
6000 features processed
7000 features processed
8000 features processed
9000 features processed
10000 features processed
11000 features processed
[4174] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
12000 features processed
13000 features processed

Any suggestion will be appreciable.

Thanks

 

 

On Mon, Apr 1, 2013 at 11:28 PM, Fields, Christopher J <[hidden email]> wrote:

Pushkala,

'###' is valid GFF3 and actually has a use (from the GFF3 spec):

-----------------------------------------
This directive (three # signs in a row) indicates that all forward references to feature IDs that have been seen to this point have been resolved. After seeing this directive, a program that is processing the file serially can close off any open objects that it has created and return them, thereby allowing iterative access to the file. Otherwise, software cannot know that a feature has been fully populated by its subfeatures until the end of the file has been reached. It is recommended that complex features, such as the canonical gene, be terminated with the ### notation.
-----------------------------------------

chris


On Apr 1, 2013, at 5:21 PM, "Jayaraman, Pushkala" <[hidden email]> wrote:

> Why do you have this “###”  in the middle in your Gff3 file?
>
> chrUn_GL339607              UCSC     chromosome     1              215         .               .               .                Name=chrUn_GL339607;ID=chrUn_GL339607
> chrUn_GL339884              UCSC     chromosome     1              195         .               .               .                Name=chrUn_GL339884;ID=chrUn_GL339884
> chrUn_GL340145              UCSC     chromosome     1              47           .               .               .                Name=chrUn_GL340145;ID=chrUn_GL340145
> ###
> chr1       refGene               gene      2625494                2628369                .               -              .                Name=PRLH;ID=PRLH;status=Provisional
> chr1       refGene               mRNA   2625494                2628369                .               -              .                Name=NM_001009434;Parent=PRLH;ID=NM_001009434;Alias=PRLH;status=Provisional
> chr1       refGene               exon      2625494                2625786                .               -              .                Name=NM_001009434.exon2;Parent=NM_001009434;ID=NM_001009434.exon2
>
> I just uploaded a part of your Gff3 file (just Chr1) onto my browser to see if it pulls up data and it does..
> So it looks like a part of Gff3 file is fine.. check what those “###” patterns are doing in your file..
>

> <image001.jpg>

>
> Pushkala
>
>
> From: Scott Cain [mailto:[hidden email]]
> Sent: Monday, April 01, 2013 10:19 AM
> To: Meenu Chopra
> Cc: Jayaraman, Pushkala; [hidden email]
> Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hi Meenu,
>
> Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.
>
> So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?
>
> When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?
>
> Scott
>
>
>
>
> On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:
> HiiI Scott , Pushkala
>
> I have  tried , what u suggest me,
>
> I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.
>
> Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.
>
> I am sending You .conf file created by me but not showing any annotation.
>
> please help me out.
>
> Thanks
>
>
>
>
> On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:
> Thanks for reminding me Pushkala: I meant to as what this was all about:
>
>   database = database_0 # do not change this!
>
> In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.
>
> Scott
>
>
> On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:
> I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.
>
> Pushkala
>
> From: Meenu Chopra [mailto:[hidden email]]
> Sent: Tuesday, March 26, 2013 12:33 AM
> To: [hidden email]
> Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hii Scott
>
> You are absolutely right, i have the same problem what you are getting.
>
> I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.
>
> Error msg:
>
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line
>
>
> ---------- Forwarded message ----------
> From: Scott Cain <[hidden email]>
> Date: Mon, Mar 25, 2013 at 5:08 PM
> Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
> To: Meenu Chopra <[hidden email]>
> Cc: [hidden email]
>
>
> Hi Meenu,
>
> Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?).
>
> Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?
>
> If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.
>
> Does your apache error log have any error messages in it that might point to the problem?
>
> Scott
>
> On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:
>
> Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.
>
> In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )
>
> I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.
>
> Please check it out once, and let me know is there any problem in .conf file or something else.
>
> Thanks
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal




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




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


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Re: error in custom track .gff uploading

Meenu



Hiiiii Pushkala, Scott

I have installed SQLite and make changes in gbrowse.conf file also, now  in log file its not showing error like:


No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.

its showing only

1000 features processed
[11129] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_44016 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.

2000 features processed
3000 features processed
4000 features processed
5000 features processed
6000 features processed
7000 features processed
8000 features processed
9000 features processed
10000 features processed
11000 features processed
[11132] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_44016 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.

12000 features processed
13000 features processed

Still its not showing any annotation on browser. I am attaching  Gbrowse.conf file.

Please look into it, and help me out.

Thanks


On Tue, Apr 2, 2013 at 10:25 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I agree with Scott.

You may also need to configure your Gbrowse to use either MYSQL or SQLite database to use that in your Gbrowse.conf.

I didn’t make any changes in the conf file or the gff3 file.

 

Pushkala

 

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, April 02, 2013 9:50 AM
To: Meenu Chopra
Cc: Fields, Christopher J; Jayaraman, Pushkala; [hidden email]
Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading

 

Meenu,

There is a message about "no upload_db_adaptor set in GBrowse.conf..." and that it is trying to use DBD::SQLite.  Do you have DBD::SQLite installed?  If not, it certainly isn't going to work since that is what it is trying to use.  You could also change the configuration to use MySQL or just use files in the files system (this is the "memory" option, the slowest of the available options).  Please see the comments in the GBrowse.conf file for guidance, as well as the documentation at http://gmod.org/wiki/GBrowse_User_Uploads.

Scott

 

On Tue, Apr 2, 2013 at 4:40 AM, Meenu Chopra <[hidden email]> wrote:

Hii Pushkala

Did u make any database for uploading that gff file or made any changes in .conf file which is generated by default.

Because I also tried to upload only chr 1 gff file,  still its not showing any annotation.

Can you Please send me that .gff and .conf file which you uploaded into custom track.

Thanks

 

On Tue, Apr 2, 2013 at 9:35 AM, Meenu Chopra <[hidden email]> wrote:

Hii Scott

For uploading only sheep .gff file I have used bp_seqfeature_load.pl command for uploading the .gff file into database, its not giving any error ( attached screen shot) .
And its running fine on browser also, apache error log does not contain any error msg, its only giving warning msg.

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet


Problem is only when I am uploading sheep file in custom track with cattle browser page, at the time of uploading sheep .gff its showing msg in error.log file.

Error msg:


No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.
No upload_db_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite. at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataLoader.pm line 355.

1000 features processed
[4172] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
2000 features processed
3000 features processed
4000 features processed
5000 features processed
6000 features processed
7000 features processed
8000 features processed
9000 features processed
10000 features processed
11000 features processed
[4174] session lock timed out on request after 10.000s
POST: http://localhost/cgi-bin/gb2/gbrowse/Bosucsc/ action=upload_status;upload_id=upload_95722 at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Session.pm line 153.
12000 features processed
13000 features processed

Any suggestion will be appreciable.

Thanks

 

 

On Mon, Apr 1, 2013 at 11:28 PM, Fields, Christopher J <[hidden email]> wrote:

Pushkala,

'###' is valid GFF3 and actually has a use (from the GFF3 spec):

-----------------------------------------
This directive (three # signs in a row) indicates that all forward references to feature IDs that have been seen to this point have been resolved. After seeing this directive, a program that is processing the file serially can close off any open objects that it has created and return them, thereby allowing iterative access to the file. Otherwise, software cannot know that a feature has been fully populated by its subfeatures until the end of the file has been reached. It is recommended that complex features, such as the canonical gene, be terminated with the ### notation.
-----------------------------------------

chris


On Apr 1, 2013, at 5:21 PM, "Jayaraman, Pushkala" <[hidden email]> wrote:

> Why do you have this “###”  in the middle in your Gff3 file?
>
> chrUn_GL339607              UCSC     chromosome     1              215         .               .               .                Name=chrUn_GL339607;ID=chrUn_GL339607
> chrUn_GL339884              UCSC     chromosome     1              195         .               .               .                Name=chrUn_GL339884;ID=chrUn_GL339884
> chrUn_GL340145              UCSC     chromosome     1              47           .               .               .                Name=chrUn_GL340145;ID=chrUn_GL340145
> ###
> chr1       refGene               gene      2625494                2628369                .               -              .                Name=PRLH;ID=PRLH;status=Provisional
> chr1       refGene               mRNA   2625494                2628369                .               -              .                Name=NM_001009434;Parent=PRLH;ID=NM_001009434;Alias=PRLH;status=Provisional
> chr1       refGene               exon      2625494                2625786                .               -              .                Name=NM_001009434.exon2;Parent=NM_001009434;ID=NM_001009434.exon2
>
> I just uploaded a part of your Gff3 file (just Chr1) onto my browser to see if it pulls up data and it does..
> So it looks like a part of Gff3 file is fine.. check what those “###” patterns are doing in your file..
>

> <image001.jpg>

>
> Pushkala
>
>
> From: Scott Cain [mailto:[hidden email]]
> Sent: Monday, April 01, 2013 10:19 AM
> To: Meenu Chopra
> Cc: Jayaraman, Pushkala; [hidden email]
> Subject: Re: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hi Meenu,
>
> Can we please back up and solve the most immediate problem first: if your hand made configuration file doesn't show any annotations then I don't think we can expect uploaded data to this data source to work either.
>
> So, why doesn't it work when you load the data into your SeqFeature::Store database?  What command did you use to load it?  Did you get any messages indicating a problem?  If you open a mysql shell, are there tables in the sheep database populated with data (even if you can't really tell what it means)?
>
> When you go to the sheep gbrowse page, do you get any messages in the apache error log?  What about on the webpage itself?
>
> Scott
>
>
>
>
> On Mon, Apr 1, 2013 at 5:22 AM, Meenu Chopra <[hidden email]> wrote:
> HiiI Scott , Pushkala
>
> I have  tried , what u suggest me,
>
> I want to tell you one thing that the .conf file which i send you earlier is not created by me, its by default created by Gbrowse only, when i am uploading .gff file conf file is uploading by default and when i am doing any changes (database name ) in that conf file , its not making any change in that , every time its showing database = database_0 # do not change this!.
>
> Without conf file its not showing track for oviari, even when i am uploading my own created  .conf file its not showing any track.
>
> I am sending You .conf file created by me but not showing any annotation.
>
> please help me out.
>
> Thanks
>
>
>
>
> On Tue, Mar 26, 2013 at 8:34 PM, Scott Cain <[hidden email]> wrote:
> Thanks for reminding me Pushkala: I meant to as what this was all about:
>
>   database = database_0 # do not change this!
>
> In general, when uploading data, I'd suggest not adding configuration until after you upload it and make sure it works, then you can add configuration to make it look the way you want.
>
> Scott
>
>
> On Tue, Mar 26, 2013 at 3:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:
> I think this is because, you haven’t defined the database name correctly.. or you do not have that in your main configuration file where you define all the databases.
>
> Pushkala
>
> From: Meenu Chopra [mailto:[hidden email]]
> Sent: Tuesday, March 26, 2013 12:33 AM
> To: [hidden email]
> Subject: [Gmod-gbrowse] Fwd: error in custom track .gff uploading
>
> Hii Scott
>
> You are absolutely right, i have the same problem what you are getting.
>
> I am attaching sheep gff file and .conf file and few lines of Apache log msg also, Please check it out once.
>
> Error msg:
>
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Can't call method "segment" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2194.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for Translation at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line 44.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Unknown database defined for DNA/GC Content at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm line 927.
> Could not open database: Can't call method "new" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataBase.pm line
>
>
> ---------- Forwarded message ----------
> From: Scott Cain <[hidden email]>
> Date: Mon, Mar 25, 2013 at 5:08 PM
> Subject: Re: [Gmod-gbrowse] error in custom track .gff uploading
> To: Meenu Chopra <[hidden email]>
> Cc: [hidden email]
>
>
> Hi Meenu,
>
> Let me make sure I understand: you have a GFF file for sheep that you wrote a configuration file for, and loaded into GBrowse, and it worked (which is what you meant when you said when you loaded the sheep data separately it was showing annotation, right?).
>
> Then, when you take the same GFF file and upload it through the browser using custom tracks/file upload, it doesn't display the annotations in the GFF file even though it seems like is should.  Is that right?
>
> If I've understood you correctly, I'm not sure why it wouldn't work either.  I noticed that the track definitions that you upload with the GFF have a track for chromosomes in it.  That strikes me as a little strange--I would think the chromosomes would already be there, so why would you be uploading them?  That might be part of the problem.  Providing us with sample GFF data the reproduces the problem might help.
>
> Does your apache error log have any error messages in it that might point to the problem?
>
> Scott
>
> On Sat, Mar 23, 2013 at 6:49 AM, Meenu Chopra <[hidden email]> wrote:
>
> Sir i have uploaded the data for Bos taurus, now i have added sheep annotation file (.gff) file and .conf file in custom track.
>
> In browser its showing the tracks for sheep but not showing any annotation for sheep genome (but when i uploaded the sheep data separately into database it was showing annotation )
>
> I have attached the sheep .conf file which i uploaded into custom track and screen shop of browser.
>
> Please check it out once, and let me know is there any problem in .conf file or something else.
>
> Thanks
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
> Meenu Chopra
> Research Associate
> Animal Genomics Lab
> NDRI, Karnal
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> Own the Future-Intel&reg; Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal




--
Meenu Chopra
Research Associate

Animal Genomics Lab
NDRI, Karnal




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




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal




--
Meenu Chopra
Research Associate
Animal Genomics Lab
NDRI, Karnal


------------------------------------------------------------------------------
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