[Gmod-gbrowse] Displaying NGS short reads problem

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[Gmod-gbrowse] Displaying NGS short reads problem

Miyajima_Nobuyuki
Hello,

We have Gbrowse2 installed.  I tried NGS Tutorial and
completed all the steps until "Displaying Summary Data",
but I only get a blank page.

However when I comment out the database entry in the [CoverageXyplot] as bellow:

[CoverageXyplot]
feature        = coverage
glyph          = wiggle_xyplot
#database       = humansamtest
height         = 50
fgcolor        = black


I am able to get the whole contents except the coverage graph.
I'm sure I have put ex1.bam and corresponding fasta file in the
designated directory, and the directory is writable and xxxx.fa.fai
file has been created.

I would appreciate any comments. Thanks.


Nobuyuki Miyajima

Frontier Research Laboratories Pharmaceutical Research Division
Takeda Pharmaceutical Company, Ltd.
10 Wadai Tsukuba Ibaraki 300-4247, JAPAN
TEL:+81-298-64-6318 FAX: +81-29-864-6308
[hidden email]

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Re: [Gmod-gbrowse] Displaying NGS short reads problem

Lincoln Stein
Hi,

Are you seeing any error messages in the Apache server error log?

Lincoln

On Tue, May 18, 2010 at 3:58 AM, <[hidden email]> wrote:
Hello,

We have Gbrowse2 installed.  I tried NGS Tutorial and
completed all the steps until "Displaying Summary Data",
but I only get a blank page.

However when I comment out the database entry in the [CoverageXyplot] as bellow:

[CoverageXyplot]
feature        = coverage
glyph          = wiggle_xyplot
#database       = humansamtest
height         = 50
fgcolor        = black


I am able to get the whole contents except the coverage graph.
I'm sure I have put ex1.bam and corresponding fasta file in the
designated directory, and the directory is writable and xxxx.fa.fai
file has been created.

I would appreciate any comments. Thanks.


Nobuyuki Miyajima

Frontier Research Laboratories Pharmaceutical Research Division
Takeda Pharmaceutical Company, Ltd.
10 Wadai Tsukuba Ibaraki 300-4247, JAPAN
TEL:+81-298-64-6318 FAX: +81-29-864-6308
[hidden email]

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: Displaying NGS short reads problem

Miyajima_Nobuyuki
Hi Lincolon,

Thank you for your quick response.
I don't see any errors in the error.log file, except the ones from the dozens of 'print STDERR'
statements I inserted in some of the modules.

The following is the messages from the 'print STDERR's  in all of the subsequent lines
of the subroutines in HTML.pm.
Just like this:

sub render_html_start {
print STDERR "IN HTML:render_html_start\n";

I only got the following 31 'IN HTML' messages:

[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_start
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_head
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_balloon_settings
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_select_menus
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_user_header
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_actionmenu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:can_generate_pdf
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_links
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_top
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_error_div
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_title
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_navbar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_search_form_objects
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:examples
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:sliderform
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:slidertable
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:zoomBar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_multiple_choices


If this information is not good enough, I would appreciate a better way.
Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, May 18, 2010 10:31 PM
To: Miyajima Nobuyuki
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Hi,

Are you seeing any error messages in the Apache server error log?

Lincoln
On Tue, May 18, 2010 at 3:58 AM, <[hidden email]> wrote:
Hello,

We have Gbrowse2 installed.  I tried NGS Tutorial and
completed all the steps until "Displaying Summary Data",
but I only get a blank page.

However when I comment out the database entry in the [CoverageXyplot] as bellow:

[CoverageXyplot]
feature        = coverage
glyph          = wiggle_xyplot
#database       = humansamtest
height         = 50
fgcolor        = black


I am able to get the whole contents except the coverage graph.
I'm sure I have put ex1.bam and corresponding fasta file in the
designated directory, and the directory is writable and xxxx.fa.fai
file has been created.

I would appreciate any comments. Thanks.


Nobuyuki Miyajima

Frontier Research Laboratories Pharmaceutical Research Division
Takeda Pharmaceutical Company, Ltd.
10 Wadai Tsukuba Ibaraki 300-4247, JAPAN
TEL:+81-298-64-6318 FAX: +81-29-864-6308
[hidden email]

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

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>
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Re: Displaying NGS short reads problem

Dave Clements, GMOD Help Desk-3
Hi Nobuyuki,

Could it be that the database is misnamed?  In the tutorial the database is named "humansam", not "humansamtest".

Dave C

On Tue, May 18, 2010 at 6:17 PM, <[hidden email]> wrote:
Hi Lincolon,

Thank you for your quick response.
I don't see any errors in the error.log file, except the ones from the dozens of 'print STDERR'
statements I inserted in some of the modules.

The following is the messages from the 'print STDERR's  in all of the subsequent lines
of the subroutines in HTML.pm.
Just like this:

sub render_html_start {
print STDERR "IN HTML:render_html_start\n";

I only got the following 31 'IN HTML' messages:

[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_start
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_head
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_balloon_settings
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_select_menus
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_user_header
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_actionmenu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:can_generate_pdf
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_links
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_top
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_error_div
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_title
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_navbar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_search_form_objects
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:examples
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:sliderform
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:slidertable
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:zoomBar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_multiple_choices


If this information is not good enough, I would appreciate a better way.
Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, May 18, 2010 10:31 PM
To: Miyajima Nobuyuki
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Hi,

Are you seeing any error messages in the Apache server error log?

Lincoln
On Tue, May 18, 2010 at 3:58 AM, <[hidden email]> wrote:
Hello,

We have Gbrowse2 installed.  I tried NGS Tutorial and
completed all the steps until "Displaying Summary Data",
but I only get a blank page.

However when I comment out the database entry in the [CoverageXyplot] as bellow:

[CoverageXyplot]
feature        = coverage
glyph          = wiggle_xyplot
#database       = humansamtest
height         = 50
fgcolor        = black


I am able to get the whole contents except the coverage graph.
I'm sure I have put ex1.bam and corresponding fasta file in the
designated directory, and the directory is writable and xxxx.fa.fai
file has been created.

I would appreciate any comments. Thanks.


Nobuyuki Miyajima

Frontier Research Laboratories Pharmaceutical Research Division
Takeda Pharmaceutical Company, Ltd.
10 Wadai Tsukuba Ibaraki 300-4247, JAPAN
TEL:+81-298-64-6318 FAX: +81-29-864-6308
[hidden email]

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

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>
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Re: Displaying NGS short reads problem

Lincoln Stein
In reply to this post by Miyajima_Nobuyuki
Actually the place where the tracks are rendered is in RenderPanels.pm, so the relevant sections are not being printed.

Do you see the individual reads when you try the next part of the tutorial? This will help isolate the problem to database vs rendering.

Lincoln

On Tue, May 18, 2010 at 9:17 PM, <[hidden email]> wrote:
Hi Lincolon,

Thank you for your quick response.
I don't see any errors in the error.log file, except the ones from the dozens of 'print STDERR'
statements I inserted in some of the modules.

The following is the messages from the 'print STDERR's  in all of the subsequent lines
of the subroutines in HTML.pm.
Just like this:

sub render_html_start {
print STDERR "IN HTML:render_html_start\n";

I only got the following 31 'IN HTML' messages:

[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_start
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_head
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_balloon_settings
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_select_menus
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_user_header
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_actionmenu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:can_generate_pdf
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_links
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_top
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_error_div
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_title
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_navbar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_search_form_objects
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:examples
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:sliderform
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:slidertable
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:zoomBar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_multiple_choices


If this information is not good enough, I would appreciate a better way.
Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, May 18, 2010 10:31 PM
To: Miyajima Nobuyuki
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Hi,

Are you seeing any error messages in the Apache server error log?

Lincoln
On Tue, May 18, 2010 at 3:58 AM, <[hidden email]> wrote:
Hello,

We have Gbrowse2 installed.  I tried NGS Tutorial and
completed all the steps until "Displaying Summary Data",
but I only get a blank page.

However when I comment out the database entry in the [CoverageXyplot] as bellow:

[CoverageXyplot]
feature        = coverage
glyph          = wiggle_xyplot
#database       = humansamtest
height         = 50
fgcolor        = black


I am able to get the whole contents except the coverage graph.
I'm sure I have put ex1.bam and corresponding fasta file in the
designated directory, and the directory is writable and xxxx.fa.fai
file has been created.

I would appreciate any comments. Thanks.


Nobuyuki Miyajima

Frontier Research Laboratories Pharmaceutical Research Division
Takeda Pharmaceutical Company, Ltd.
10 Wadai Tsukuba Ibaraki 300-4247, JAPAN
TEL:+81-298-64-6318 FAX: +81-29-864-6308
[hidden email]

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

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



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: Displaying NGS short reads problem

Miyajima_Nobuyuki
Hi, Lincoln

I finally got the page after modifying the gff files and reloaded into the database,  but the Coverage(xyplot) is not shown.
Using CoverageDensity, a full-range blue box is displayed.
I have no problem showing individual reads.


Hi, David,
>Could it be that the database is misnamed?  In the tutorial the database is named "humansam", not "humansamtest".

I named my sam database 'humansamtest' as follows:

[humansamtest:database]
db_adaptor     = Bio::DB::Sam

and the problem is not solved even when I changed the name to 'humansam'.

Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Friday, May 21, 2010 11:16 PM
To: Miyajima Nobuyuki/医薬研究開拓研主席研究員
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Actually the place where the tracks are rendered is in RenderPanels.pm, so the relevant sections are not being printed.

Do you see the individual reads when you try the next part of the tutorial? This will help isolate the problem to database vs rendering.

Lincoln
On Tue, May 18, 2010 at 9:17 PM, <[hidden email]> wrote:
Hi Lincolon,

Thank you for your quick response.
I don't see any errors in the error.log file, except the ones from the dozens of 'print STDERR'
statements I inserted in some of the modules.

The following is the messages from the 'print STDERR's  in all of the subsequent lines
of the subroutines in HTML.pm.
Just like this:

sub render_html_start {
print STDERR "IN HTML:render_html_start\n";

I only got the following 31 'IN HTML' messages:

[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_start
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_head
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_balloon_settings
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_select_menus
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_user_header
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_actionmenu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:can_generate_pdf
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_links
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_top
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_error_div
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_title
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_navbar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_search_form_objects
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:examples
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:sliderform
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:slidertable
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:zoomBar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_multiple_choices


If this information is not good enough, I would appreciate a better way.
Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, May 18, 2010 10:31 PM
To: Miyajima Nobuyuki
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Hi,

Are you seeing any error messages in the Apache server error log?

Lincoln
On Tue, May 18, 2010 at 3:58 AM, <[hidden email]> wrote:
Hello,

We have Gbrowse2 installed.  I tried NGS Tutorial and
completed all the steps until "Displaying Summary Data",
but I only get a blank page.

However when I comment out the database entry in the [CoverageXyplot] as bellow:

[CoverageXyplot]
feature        = coverage
glyph          = wiggle_xyplot
#database       = humansamtest
height         = 50
fgcolor        = black


I am able to get the whole contents except the coverage graph.
I'm sure I have put ex1.bam and corresponding fasta file in the
designated directory, and the directory is writable and xxxx.fa.fai
file has been created.

I would appreciate any comments. Thanks.


Nobuyuki Miyajima

Frontier Research Laboratories Pharmaceutical Research Division
Takeda Pharmaceutical Company, Ltd.
10 Wadai Tsukuba Ibaraki 300-4247, JAPAN
TEL:+81-298-64-6318 FAX: +81-29-864-6308
[hidden email]

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

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>
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Re: Displaying NGS short reads problem

Dave Clements, GMOD Help Desk-3
Hi Nobuyuki,

I don't know what is going on here.  Have you tried explicitly setting things like max_score, min_score, bicolor_pivot, pos_color, and neg_color?  That might help shed some light on where the problem is, or lead to a workaround.

Dave C.



On Mon, May 24, 2010 at 2:24 AM, <[hidden email]> wrote:
Hi, Lincoln

I finally got the page after modifying the gff files and reloaded into the database,  but the Coverage(xyplot) is not shown.
Using CoverageDensity, a full-range blue box is displayed.
I have no problem showing individual reads.


Hi, David,
>Could it be that the database is misnamed?  In the tutorial the database is named "humansam", not "humansamtest".

I named my sam database 'humansamtest' as follows:

[humansamtest:database]
db_adaptor     = Bio::DB::Sam

and the problem is not solved even when I changed the name to 'humansam'.

Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Friday, May 21, 2010 11:16 PM
To: Miyajima Nobuyuki/医薬研究開拓研主席研究員
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Actually the place where the tracks are rendered is in RenderPanels.pm, so the relevant sections are not being printed.

Do you see the individual reads when you try the next part of the tutorial? This will help isolate the problem to database vs rendering.

Lincoln
On Tue, May 18, 2010 at 9:17 PM, <[hidden email]> wrote:
Hi Lincolon,

Thank you for your quick response.
I don't see any errors in the error.log file, except the ones from the dozens of 'print STDERR'
statements I inserted in some of the modules.

The following is the messages from the 'print STDERR's  in all of the subsequent lines
of the subroutines in HTML.pm.
Just like this:

sub render_html_start {
print STDERR "IN HTML:render_html_start\n";

I only got the following 31 'IN HTML' messages:

[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_start
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_head
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_balloon_settings
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_select_menus
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_user_header
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_actionmenu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:can_generate_pdf
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_links
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_top
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_error_div
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_title
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_navbar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_search_form_objects
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:examples
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:sliderform
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:slidertable
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:zoomBar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_multiple_choices


If this information is not good enough, I would appreciate a better way.
Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, May 18, 2010 10:31 PM
To: Miyajima Nobuyuki
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Hi,

Are you seeing any error messages in the Apache server error log?

Lincoln
On Tue, May 18, 2010 at 3:58 AM, <[hidden email]> wrote:
Hello,

We have Gbrowse2 installed.  I tried NGS Tutorial and
completed all the steps until "Displaying Summary Data",
but I only get a blank page.

However when I comment out the database entry in the [CoverageXyplot] as bellow:

[CoverageXyplot]
feature        = coverage
glyph          = wiggle_xyplot
#database       = humansamtest
height         = 50
fgcolor        = black


I am able to get the whole contents except the coverage graph.
I'm sure I have put ex1.bam and corresponding fasta file in the
designated directory, and the directory is writable and xxxx.fa.fai
file has been created.

I would appreciate any comments. Thanks.


Nobuyuki Miyajima

Frontier Research Laboratories Pharmaceutical Research Division
Takeda Pharmaceutical Company, Ltd.
10 Wadai Tsukuba Ibaraki 300-4247, JAPAN
TEL:+81-298-64-6318 FAX: +81-29-864-6308
[hidden email]

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

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



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>
------------------------------------------------------------------------------

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===> PLEASE KEEP RESPONSES ON THE LIST <===
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Re: Displaying NGS short reads problem

Lincoln Stein
In reply to this post by Miyajima_Nobuyuki
Hi Scott,

Could you check that the NGS tutorial is working as it is supposed to? 

Lincoln

On Mon, May 24, 2010 at 2:24 AM, <[hidden email]> wrote:
Hi, Lincoln

I finally got the page after modifying the gff files and reloaded into the database,  but the Coverage(xyplot) is not shown.
Using CoverageDensity, a full-range blue box is displayed.
I have no problem showing individual reads.


Hi, David,
>Could it be that the database is misnamed?  In the tutorial the database is named "humansam", not "humansamtest".

I named my sam database 'humansamtest' as follows:

[humansamtest:database]
db_adaptor     = Bio::DB::Sam

and the problem is not solved even when I changed the name to 'humansam'.

Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Friday, May 21, 2010 11:16 PM
To: Miyajima Nobuyuki/医薬研究開拓研主席研究員
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Actually the place where the tracks are rendered is in RenderPanels.pm, so the relevant sections are not being printed.

Do you see the individual reads when you try the next part of the tutorial? This will help isolate the problem to database vs rendering.

Lincoln
On Tue, May 18, 2010 at 9:17 PM, <[hidden email]> wrote:
Hi Lincolon,

Thank you for your quick response.
I don't see any errors in the error.log file, except the ones from the dozens of 'print STDERR'
statements I inserted in some of the modules.

The following is the messages from the 'print STDERR's  in all of the subsequent lines
of the subroutines in HTML.pm.
Just like this:

sub render_html_start {
print STDERR "IN HTML:render_html_start\n";

I only got the following 31 'IN HTML' messages:

[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_start
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_head
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_balloon_settings
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_select_menus
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_user_header
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_actionmenu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:can_generate_pdf
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_links
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_top
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_error_div
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_title
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_navbar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_search_form_objects
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:examples
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:sliderform
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:slidertable
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:zoomBar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_multiple_choices


If this information is not good enough, I would appreciate a better way.
Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, May 18, 2010 10:31 PM
To: Miyajima Nobuyuki
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Hi,

Are you seeing any error messages in the Apache server error log?

Lincoln
On Tue, May 18, 2010 at 3:58 AM, <[hidden email]> wrote:
Hello,

We have Gbrowse2 installed.  I tried NGS Tutorial and
completed all the steps until "Displaying Summary Data",
but I only get a blank page.

However when I comment out the database entry in the [CoverageXyplot] as bellow:

[CoverageXyplot]
feature        = coverage
glyph          = wiggle_xyplot
#database       = humansamtest
height         = 50
fgcolor        = black


I am able to get the whole contents except the coverage graph.
I'm sure I have put ex1.bam and corresponding fasta file in the
designated directory, and the directory is writable and xxxx.fa.fai
file has been created.

I would appreciate any comments. Thanks.


Nobuyuki Miyajima

Frontier Research Laboratories Pharmaceutical Research Division
Takeda Pharmaceutical Company, Ltd.
10 Wadai Tsukuba Ibaraki 300-4247, JAPAN
TEL:+81-298-64-6318 FAX: +81-29-864-6308
[hidden email]

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

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



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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


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Re: Displaying NGS short reads problem

Lincoln Stein
In reply to this post by Miyajima_Nobuyuki
Could you cut-and-paste your configuration sections (the read coverage stanza and the database stanza) into another email. There must be a subtle issue.

Lincoln

On Mon, May 24, 2010 at 2:24 AM, <[hidden email]> wrote:
Hi, Lincoln

I finally got the page after modifying the gff files and reloaded into the database,  but the Coverage(xyplot) is not shown.
Using CoverageDensity, a full-range blue box is displayed.
I have no problem showing individual reads.


Hi, David,
>Could it be that the database is misnamed?  In the tutorial the database is named "humansam", not "humansamtest".

I named my sam database 'humansamtest' as follows:

[humansamtest:database]
db_adaptor     = Bio::DB::Sam

and the problem is not solved even when I changed the name to 'humansam'.

Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Friday, May 21, 2010 11:16 PM
To: Miyajima Nobuyuki/医薬研究開拓研主席研究員
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Actually the place where the tracks are rendered is in RenderPanels.pm, so the relevant sections are not being printed.

Do you see the individual reads when you try the next part of the tutorial? This will help isolate the problem to database vs rendering.

Lincoln
On Tue, May 18, 2010 at 9:17 PM, <[hidden email]> wrote:
Hi Lincolon,

Thank you for your quick response.
I don't see any errors in the error.log file, except the ones from the dozens of 'print STDERR'
statements I inserted in some of the modules.

The following is the messages from the 'print STDERR's  in all of the subsequent lines
of the subroutines in HTML.pm.
Just like this:

sub render_html_start {
print STDERR "IN HTML:render_html_start\n";

I only got the following 31 'IN HTML' messages:

[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_start
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_html_head
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_balloon_settings
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_select_menus
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:_render_select_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_user_header
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_actionmenu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:can_generate_pdf
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_links
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_top
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_error_div
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_title
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_navbar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_search_form_objects
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:examples
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:plugin_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_form
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:source_menu
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:sliderform
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:slidertable
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:zoomBar
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:html_frag
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:toggle_section
[Wed May 19 09:18:30 2010] [error] [client XXX.XXX.XXX.XXX] IN HTML:render_multiple_choices


If this information is not good enough, I would appreciate a better way.
Thanks.

Nobuyuki


From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, May 18, 2010 10:31 PM
To: Miyajima Nobuyuki
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

Hi,

Are you seeing any error messages in the Apache server error log?

Lincoln
On Tue, May 18, 2010 at 3:58 AM, <[hidden email]> wrote:
Hello,

We have Gbrowse2 installed.  I tried NGS Tutorial and
completed all the steps until "Displaying Summary Data",
but I only get a blank page.

However when I comment out the database entry in the [CoverageXyplot] as bellow:

[CoverageXyplot]
feature        = coverage
glyph          = wiggle_xyplot
#database       = humansamtest
height         = 50
fgcolor        = black


I am able to get the whole contents except the coverage graph.
I'm sure I have put ex1.bam and corresponding fasta file in the
designated directory, and the directory is writable and xxxx.fa.fai
file has been created.

I would appreciate any comments. Thanks.


Nobuyuki Miyajima

Frontier Research Laboratories Pharmaceutical Research Division
Takeda Pharmaceutical Company, Ltd.
10 Wadai Tsukuba Ibaraki 300-4247, JAPAN
TEL:+81-298-64-6318 FAX: +81-29-864-6308
[hidden email]

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

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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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


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Re: Displaying NGS short reads problem

Miyajima_Nobuyuki

Hi  Lincoln,

 

The config file is as follows and the screenshot is attached. I use only chr20.

 

I also noticed that I'm not able to see an alignment using samtools like this:

 

>samtools tview ex1chr20.bam chr20.fa

 

but

 

>samtools pileup -cf chr20.fa ex1chr20.bam

 

is OK.

 

 

Nobuyuki

 

 

 

[GENERAL]

description   = Human Chromosomes 20

database      = annotations

 

initial landmark = chr20:67960..69550

 

default tracks = PredictedGenes

 

# examples to show in the introduction

examples = chr20:67960..69559

 

# bring in the special Submitter plugin

plugins   = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper Submitter

 

# "automatic" classes to try when an unqualified identifier is given

# automatic classes = Symbol Gene Clone

 

#################################

# database definitions

#################################

 

[annotations:database]

db_adaptor     = Bio::DB::SeqFeature::Store

db_args        = -adaptor DBI::mysql

                                                     -dsn human      dbi:mysql:database=human;host=localhost

                 -user    miyajima

 

search options = default +autocomplete

 

 

 

[humansam:database]

db_adaptor     = Bio::DB::Sam

db_args        = -fasta /data2/gbrowse2/htdocs/databases/humansam/chr20.fa

                 -bam   /data2/gbrowse2/htdocs/databases/humansam/ex1chr20.bam

 

search options = default

 

 

# Advanced feature: custom balloons

custom balloons = [balloon]

                  delayTime = 500

 

                  [balloon500]

                                                                                                                                        maxWidth  = 500

                  delayTime = 50

 

 

# Advanced feature: an example of callbacks to be run remotely

# by gbrowse_details for AJAX/iframe balloons

[TOOLTIPS]

intro = sub {

                my $args  = shift;

                my $feat  = $args->{feature};

                my $name  = $feat->display_name;

                my $type  = $feat->primary_tag;

                my $class = $feat->class;

                my $extra = join(' ',$feat->each_tag_value('Note')) if $feat->has_tag('Note');

                my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';

                my $msg   = "Hello, I am $name, a$n $type of class $class";

                $msg     .= "<br>I am described as a <i><b>$extra</b></i>" if $extra;

                $msg     .= "<br>Click to see the sequence of $name";

                return "<table><tr><th bgcolor='lightsteelblue'>$name</th><tr>" .

                       "<tr><td>$msg</td></tr></table>";

           }

full_sequence = sub {

                                                     my $args = shift;

                                               my $feat = $args->{feature};

                                                                         my $name  = $feat->display_name;

                                                                                                                 my $seq = $feat->seq->seq;

                 $seq =~ s/(\S{75})/$1\n/g;

                 return "<pre style='font-size:8pt'>>$name\n$seq</pre>";

               }

 

# Advanced feature:

# Pop up rubberband menus for submitting selected region to search engines...

#include "detail_select_menu.conf"

#include "submitter_plugin.conf"

 

# Default glyph settings

[TRACK DEFAULTS]

glyph       = generic

database    = annotations

height      = 8

bgcolor     = cyan

fgcolor     = black

label density = 25

bump density  = 100

# default pop-up balloon

balloon hover = <b>$name</b> is a $type spanning $ref from $start to $end. Click for more details.

 

### TRACK CONFIGURATION ####

# the remainder of the sections configure individual tracks

 

[DNA]

glyph          = dna

global feature = 1

height         = 40

do_gc          = 1

category       = Basic features

gc_window      = auto

strand         = both

fgcolor        = red

axis_color     = blue

discoverable   = 0

key            = DNA

 

[Translation]

glyph          = translation

global feature = 1

height         = 40

category       = Basic features

fgcolor        = purple

strand         = +1

translation    = 6frame

key            = 6-frame translation

 

[PredictedGenes]

feature        = mRNA

glyph          = so_transcript

description    = 1

bgcolor        = beige

category       = Basic features

key            = Ensembl predicted genes

 

[CoverageXyplot]

feature        = coverage

glyph          = wiggle_xyplot

database       = humansam

height         = 50

fgcolor        = black

bicolor_pivot  = 20

pos_color      = blue

neg_color      = red

key            = Coverage (xyplot)

category       = Reads

label          = 0 # Labels on wiggle tracks are redundant.

 

[CoverageDensity]

feature       = coverage

glyph         = wiggle_density

database      = humansam

height        = 30

bgcolor       = blue

bicolor_pivot = 20

pos_color     = blue

neg_color     = red

key           = Coverage (density plot)

category      = Reads

label         = 0 # labels on wiggle tracks are redundant

 

[Reads]

feature        = match

glyph          = segments

draw_target    = 1

show_mismatch  = 1

mismatch_color = red

database       = humansam

bgcolor        = blue

fgcolor        = white

height         = 5

label density  = 50

bump           = fast

key            = Reads

category       = Reads

 

 

gbrowse2_100526-s1.png

 

 

 

 

 

From: Lincoln Stein [mailto:[hidden email]]
Sent: Wednesday, May 26, 2010 9:22 AM
To: Miyajima Nobuyuki/
医薬研究開拓研主席研究員
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

 

Could you cut-and-paste your configuration sections (the read coverage stanza and the database stanza) into another email. There must be a subtle issue.

 

Lincoln

 


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Displaying NGS short reads problem

Miyajima_Nobuyuki
In reply to this post by Miyajima_Nobuyuki
Hi,

I've created a small database using an attached 12-line gff file(ex1.gff),  
a conf file(ex1.conf) and ex1.sam and ex1.fa files from samtools example.
I haven't changed any part of the ex1.sam file, and I'm still not able
to get a Coverage plot as in the attachecd png file.
I don't see any errors in the error.log file.
I use Gbrowse2.08, Bio::Graphics 2.09 and Bio-Samtools 1.19.


I'd appreciate any help.

Nobuyuki


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gbrowse2_100528.png (68K) Download Attachment
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Re: Displaying NGS short reads problem

Wes Barris
On 28/05/2010 7:46 PM, [hidden email] wrote:
> Hi,
>
> I've created a small database using an attached 12-line gff file(ex1.gff),
> a conf file(ex1.conf) and ex1.sam and ex1.fa files from samtools example.
> I haven't changed any part of the ex1.sam file, and I'm still not able
> to get a Coverage plot as in the attachecd png file.
> I don't see any errors in the error.log file.
> I use Gbrowse2.08, Bio::Graphics 2.09 and Bio-Samtools 1.19.

I tried your .conf file on our system with one of our .bam files and it properly
displayed the CoverageXyplot.  I am running the same versions of software
that you are.  I'm not sure what this tells you other than your .conf file is
ok and the software works for me.

> I'd appreciate any help.
>
> Nobuyuki
>


--
Wes Barris

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Re: Displaying NGS short reads problem

Miyajima_Nobuyuki
Hi,

I installed everything in another machine, and confirmed everything works fine without any problems.
I'll let you know when I get to the cause of the problem.
Thank you for all your help.

Nbobuyuki Miyajima

-----Original Message-----
From: Wes Barris [mailto:[hidden email]]
Sent: Monday, May 31, 2010 9:23 AM
To: Miyajima Nobuyuki
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

On 28/05/2010 7:46 PM, [hidden email] wrote:
> Hi,
>
> I've created a small database using an attached 12-line gff file(ex1.gff),
> a conf file(ex1.conf) and ex1.sam and ex1.fa files from samtools example.
> I haven't changed any part of the ex1.sam file, and I'm still not able
> to get a Coverage plot as in the attachecd png file.
> I don't see any errors in the error.log file.
> I use Gbrowse2.08, Bio::Graphics 2.09 and Bio-Samtools 1.19.

I tried your .conf file on our system with one of our .bam files and it properly
displayed the CoverageXyplot.  I am running the same versions of software
that you are.  I'm not sure what this tells you other than your .conf file is
ok and the software works for me.

> I'd appreciate any help.
>
> Nobuyuki
>


--
Wes Barris

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Re: Displaying NGS short reads problem

Lincoln Stein
This type of mysterious database opening failure reminds me of SELINUX issues. Are you using a distribution such as RedHat that uses SELINUX access control lists?

Lincoln

On Tue, Jun 1, 2010 at 1:26 AM, <[hidden email]> wrote:
Hi,

I installed everything in another machine, and confirmed everything works fine without any problems.
I'll let you know when I get to the cause of the problem.
Thank you for all your help.

Nbobuyuki Miyajima

-----Original Message-----
From: Wes Barris [mailto:[hidden email]]
Sent: Monday, May 31, 2010 9:23 AM
To: Miyajima Nobuyuki
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Displaying NGS short reads problem

On 28/05/2010 7:46 PM, [hidden email] wrote:
> Hi,
>
> I've created a small database using an attached 12-line gff file(ex1.gff),
> a conf file(ex1.conf) and ex1.sam and ex1.fa files from samtools example.
> I haven't changed any part of the ex1.sam file, and I'm still not able
> to get a Coverage plot as in the attachecd png file.
> I don't see any errors in the error.log file.
> I use Gbrowse2.08, Bio::Graphics 2.09 and Bio-Samtools 1.19.

I tried your .conf file on our system with one of our .bam files and it properly
displayed the CoverageXyplot.  I am running the same versions of software
that you are.  I'm not sure what this tells you other than your .conf file is
ok and the software works for me.

> I'd appreciate any help.
>
> Nobuyuki
>


--
Wes Barris

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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