Re: GBrowse visualization problem

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Re: GBrowse visualization problem

Scott Cain
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <[hidden email]> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



--
------------------------------------------------------------------------
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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Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk
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Re: GBrowse visualization problem

Bob Muller-2
Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a href="javascript:_e({}, &#39;cvml&#39;, &#39;tberardi@acoma.stanford.edu&#39;);" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



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

------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk
_______________________________________________
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Re: GBrowse visualization problem

Bob Muller
In reply to this post by Scott Cain
Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a href="javascript:_e({}, 'cvml', 'tberardi@acoma.stanford.edu');" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



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

------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
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Re: GBrowse visualization problem

Bob Muller
In reply to this post by Scott Cain
Scott,

The track loading problem that Tanya mentioned turned out to be the fact that the / mount had completely filled up. I cleared out the apache logs and got 2GB freed, and the user was able to load. But then the hanging problems started, and presumably the NaN. Could the freezeup due to the disk-full problem have caused an issue somewhere in the temporary files that gbrowse creates? Where might I look?
  --Bob Muller

Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a href="javascript:_e({}, 'cvml', 'tberardi@acoma.stanford.edu');" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



--
------------------------------------------------------------------------
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: GBrowse visualization problem

Bob Muller-2
I've cleared the current cache, quite large. No effect. We've noticed memory is a bit low,

             total       used       free     shared    buffers     cached
Mem:       3924572    3738124     186448          0    1948260     948328

but there's no swapping, so I don't really think that's the problem. We'll increase it in the VM next week to be sure.

I still get the same error messages in the Apache log trying the samples.

Any other suggestions where to look?

Scott, I'm not sure which link got you to your NaN URL, I haven't been able to reproduce that. Can you give me more detail?

  --Bob

On 10/4/13 1:31 PM, Bob Muller wrote:
Scott,

The track loading problem that Tanya mentioned turned out to be the fact that the / mount had completely filled up. I cleared out the apache logs and got 2GB freed, and the user was able to load. But then the hanging problems started, and presumably the NaN. Could the freezeup due to the disk-full problem have caused an issue somewhere in the temporary files that gbrowse creates? Where might I look?
  --Bob Muller

Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a moz-do-not-send="true" href="javascript:_e({}, 'cvml', 'tberardi@acoma.stanford.edu');" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



--
------------------------------------------------------------------------
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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Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk


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Re: GBrowse visualization problem

Bob Muller
In reply to this post by Bob Muller
I've cleared the current cache, quite large. No effect. We've noticed memory is a bit low,

             total       used       free     shared    buffers     cached
Mem:       3924572    3738124     186448          0    1948260     948328

but there's no swapping, so I don't really think that's the problem. We'll increase it in the VM next week to be sure.

I still get the same error messages in the Apache log trying the samples.

Any other suggestions where to look?

Scott, I'm not sure which link got you to your NaN URL, I haven't been able to reproduce that. Can you give me more detail?

  --Bob

On 10/4/13 1:31 PM, Bob Muller wrote:
Scott,

The track loading problem that Tanya mentioned turned out to be the fact that the / mount had completely filled up. I cleared out the apache logs and got 2GB freed, and the user was able to load. But then the hanging problems started, and presumably the NaN. Could the freezeup due to the disk-full problem have caused an issue somewhere in the temporary files that gbrowse creates? Where might I look?
  --Bob Muller

Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a moz-do-not-send="true" href="javascript:_e({}, 'cvml', 'tberardi@acoma.stanford.edu');" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



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


------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk


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the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk
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Re: GBrowse visualization problem

Bob Muller-2
Also, the symptoms are client-side: doing these operations in Chrome works fine, but doing them in Firefox or Internet Explorer 9 seems to fail most of the time.

  --Bob

On 10/4/13 9:30 PM, Bob Muller wrote:
I've cleared the current cache, quite large. No effect. We've noticed memory is a bit low,

             total       used       free     shared    buffers     cached
Mem:       3924572    3738124     186448          0    1948260     948328

but there's no swapping, so I don't really think that's the problem. We'll increase it in the VM next week to be sure.

I still get the same error messages in the Apache log trying the samples.

Any other suggestions where to look?

Scott, I'm not sure which link got you to your NaN URL, I haven't been able to reproduce that. Can you give me more detail?

  --Bob

On 10/4/13 1:31 PM, Bob Muller wrote:
Scott,

The track loading problem that Tanya mentioned turned out to be the fact that the / mount had completely filled up. I cleared out the apache logs and got 2GB freed, and the user was able to load. But then the hanging problems started, and presumably the NaN. Could the freezeup due to the disk-full problem have caused an issue somewhere in the temporary files that gbrowse creates? Where might I look?
  --Bob Muller

Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a moz-do-not-send="true" href="javascript:_e({}, 'cvml', 'tberardi@acoma.stanford.edu');" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



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


------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk


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------------------------------------------------------------------------------
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Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
the latest Intel processors and coprocessors. See abstracts and register >
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Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
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Re: GBrowse visualization problem

Bob Muller
In reply to this post by Bob Muller
Also, the symptoms are client-side: doing these operations in Chrome works fine, but doing them in Firefox or Internet Explorer 9 seems to fail most of the time.

  --Bob

On 10/4/13 9:30 PM, Bob Muller wrote:
I've cleared the current cache, quite large. No effect. We've noticed memory is a bit low,

             total       used       free     shared    buffers     cached
Mem:       3924572    3738124     186448          0    1948260     948328

but there's no swapping, so I don't really think that's the problem. We'll increase it in the VM next week to be sure.

I still get the same error messages in the Apache log trying the samples.

Any other suggestions where to look?

Scott, I'm not sure which link got you to your NaN URL, I haven't been able to reproduce that. Can you give me more detail?

  --Bob

On 10/4/13 1:31 PM, Bob Muller wrote:
Scott,

The track loading problem that Tanya mentioned turned out to be the fact that the / mount had completely filled up. I cleared out the apache logs and got 2GB freed, and the user was able to load. But then the hanging problems started, and presumably the NaN. Could the freezeup due to the disk-full problem have caused an issue somewhere in the temporary files that gbrowse creates? Where might I look?
  --Bob Muller

Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a moz-do-not-send="true" href="javascript:_e({}, 'cvml', 'tberardi@acoma.stanford.edu');" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



--
------------------------------------------------------------------------
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: GBrowse visualization problem

Bob Muller-2
After debugging extensively on the server side, I can't find anything in the system other than the error messages already reported. Memory use is fine, there are no delays in serving data etc.

So, to sum up, TAIR GBrowse works fine on Chrome but fails in some Firefox and Internet Explorer browsers, with the symptom being display of headers and track headers but no display of actual track images, just a working icon flashing in the upper left corner. The error logs (see Tanya's included email below) show error messages which are unresolved at this time.

Does anyone have any suggestions where to look next?
  --Bob Muller

On 10/5/13 4:30 PM, Bob Muller wrote:
Also, the symptoms are client-side: doing these operations in Chrome works fine, but doing them in Firefox or Internet Explorer 9 seems to fail most of the time.

  --Bob

On 10/4/13 9:30 PM, Bob Muller wrote:
I've cleared the current cache, quite large. No effect. We've noticed memory is a bit low,

             total       used       free     shared    buffers     cached
Mem:       3924572    3738124     186448          0    1948260     948328

but there's no swapping, so I don't really think that's the problem. We'll increase it in the VM next week to be sure.

I still get the same error messages in the Apache log trying the samples.

Any other suggestions where to look?

Scott, I'm not sure which link got you to your NaN URL, I haven't been able to reproduce that. Can you give me more detail?

  --Bob

On 10/4/13 1:31 PM, Bob Muller wrote:
Scott,

The track loading problem that Tanya mentioned turned out to be the fact that the / mount had completely filled up. I cleared out the apache logs and got 2GB freed, and the user was able to load. But then the hanging problems started, and presumably the NaN. Could the freezeup due to the disk-full problem have caused an issue somewhere in the temporary files that gbrowse creates? Where might I look?
  --Bob Muller

Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a moz-do-not-send="true" href="javascript:_e({}, 'cvml', 'tberardi@acoma.stanford.edu');" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



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


------------------------------------------------------------------------------
October Webinars: Code for Performance
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Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk


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Re: GBrowse visualization problem

Bob Muller
In reply to this post by Bob Muller
After debugging extensively on the server side, I can't find anything in the system other than the error messages already reported. Memory use is fine, there are no delays in serving data etc.

So, to sum up, TAIR GBrowse works fine on Chrome but fails in some Firefox and Internet Explorer browsers, with the symptom being display of headers and track headers but no display of actual track images, just a working icon flashing in the upper left corner. The error logs (see Tanya's included email below) show error messages which are unresolved at this time.

Does anyone have any suggestions where to look next?
  --Bob Muller

On 10/5/13 4:30 PM, Bob Muller wrote:
Also, the symptoms are client-side: doing these operations in Chrome works fine, but doing them in Firefox or Internet Explorer 9 seems to fail most of the time.

  --Bob

On 10/4/13 9:30 PM, Bob Muller wrote:
I've cleared the current cache, quite large. No effect. We've noticed memory is a bit low,

             total       used       free     shared    buffers     cached
Mem:       3924572    3738124     186448          0    1948260     948328

but there's no swapping, so I don't really think that's the problem. We'll increase it in the VM next week to be sure.

I still get the same error messages in the Apache log trying the samples.

Any other suggestions where to look?

Scott, I'm not sure which link got you to your NaN URL, I haven't been able to reproduce that. Can you give me more detail?

  --Bob

On 10/4/13 1:31 PM, Bob Muller wrote:
Scott,

The track loading problem that Tanya mentioned turned out to be the fact that the / mount had completely filled up. I cleared out the apache logs and got 2GB freed, and the user was able to load. But then the hanging problems started, and presumably the NaN. Could the freezeup due to the disk-full problem have caused an issue somewhere in the temporary files that gbrowse creates? Where might I look?
  --Bob Muller

Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a moz-do-not-send="true" href="javascript:_e({}, 'cvml', 'tberardi@acoma.stanford.edu');" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



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


------------------------------------------------------------------------------
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
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Re: GBrowse visualization problem

Jim Hu
In reply to this post by Bob Muller-2
I'm guessing that you're working on it, as the behavior changed in the last few minutes. 

Before that I got the same 500 error in Chrome (Version 30.0.1599.69 on a MacBook Air). 


On Oct 8, 2013, at 5:10 AM, Bob Muller wrote:

After debugging extensively on the server side, I can't find anything in the system other than the error messages already reported. Memory use is fine, there are no delays in serving data etc.

So, to sum up, TAIR GBrowse works fine on Chrome but fails in some Firefox and Internet Explorer browsers, with the symptom being display of headers and track headers but no display of actual track images, just a working icon flashing in the upper left corner. The error logs (see Tanya's included email below) show error messages which are unresolved at this time.

Does anyone have any suggestions where to look next?
  --Bob Muller

On 10/5/13 4:30 PM, Bob Muller wrote:
Also, the symptoms are client-side: doing these operations in Chrome works fine, but doing them in Firefox or Internet Explorer 9 seems to fail most of the time.

  --Bob

On 10/4/13 9:30 PM, Bob Muller wrote:
I've cleared the current cache, quite large. No effect. We've noticed memory is a bit low,

             total       used       free     shared    buffers     cached
Mem:       3924572    3738124     186448          0    1948260     948328

but there's no swapping, so I don't really think that's the problem. We'll increase it in the VM next week to be sure.

I still get the same error messages in the Apache log trying the samples.

Any other suggestions where to look?

Scott, I'm not sure which link got you to your NaN URL, I haven't been able to reproduce that. Can you give me more detail?

  --Bob

On 10/4/13 1:31 PM, Bob Muller wrote:
Scott,

The track loading problem that Tanya mentioned turned out to be the fact that the / mount had completely filled up. I cleared out the apache logs and got 2GB freed, and the user was able to load. But then the hanging problems started, and presumably the NaN. Could the freezeup due to the disk-full problem have caused an issue somewhere in the temporary files that gbrowse creates? Where might I look?
  --Bob Muller

Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a moz-do-not-send="true" href="javascript:_e({},%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20'cvml',%20'tberardi@acoma.stanford.edu');" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



--
------------------------------------------------------------------------
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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Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054



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Re: GBrowse visualization problem

Bob Muller
The 500 error probably came from a restart of the virtual machine yesterday, to increase memory. That happened around 3:49 central time. Not sure why the error might have persisted, perhaps caching? Nothing has been done to the server in the last 15 hours.

In any case, the problem people are experiencing is a hang while trying to display the images, all the headers and so on come up fine, in Firefox. Chrome displays all the images just fine.

  --Bob

On 10/8/13 8:00 AM, Jim Hu wrote:
I'm guessing that you're working on it, as the behavior changed in the last few minutes. 

Before that I got the same 500 error in Chrome (Version 30.0.1599.69 on a MacBook Air). 


On Oct 8, 2013, at 5:10 AM, Bob Muller wrote:

After debugging extensively on the server side, I can't find anything in the system other than the error messages already reported. Memory use is fine, there are no delays in serving data etc.

So, to sum up, TAIR GBrowse works fine on Chrome but fails in some Firefox and Internet Explorer browsers, with the symptom being display of headers and track headers but no display of actual track images, just a working icon flashing in the upper left corner. The error logs (see Tanya's included email below) show error messages which are unresolved at this time.

Does anyone have any suggestions where to look next?
  --Bob Muller

On 10/5/13 4:30 PM, Bob Muller wrote:
Also, the symptoms are client-side: doing these operations in Chrome works fine, but doing them in Firefox or Internet Explorer 9 seems to fail most of the time.

  --Bob

On 10/4/13 9:30 PM, Bob Muller wrote:
I've cleared the current cache, quite large. No effect. We've noticed memory is a bit low,

             total       used       free     shared    buffers     cached
Mem:       3924572    3738124     186448          0    1948260     948328

but there's no swapping, so I don't really think that's the problem. We'll increase it in the VM next week to be sure.

I still get the same error messages in the Apache log trying the samples.

Any other suggestions where to look?

Scott, I'm not sure which link got you to your NaN URL, I haven't been able to reproduce that. Can you give me more detail?

  --Bob

On 10/4/13 1:31 PM, Bob Muller wrote:
Scott,

The track loading problem that Tanya mentioned turned out to be the fact that the / mount had completely filled up. I cleared out the apache logs and got 2GB freed, and the user was able to load. But then the hanging problems started, and presumably the NaN. Could the freezeup due to the disk-full problem have caused an issue somewhere in the temporary files that gbrowse creates? Where might I look?
  --Bob Muller

Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <<a moz-do-not-send="true" href="javascript:_e({},%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20'cvml',%20'tberardi@acoma.stanford.edu');" target="_blank">tberardi@...> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



--
------------------------------------------------------------------------
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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2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054




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Re: GBrowse visualization problem

Tanya Berardini
In reply to this post by Bob Muller
I am not getting any display of tracks on Chrome.  Exactly the same (non) view as on Firefox.

Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================


On Fri, Oct 4, 2013 at 9:30 PM, Bob Muller <[hidden email]> wrote:
I've cleared the current cache, quite large. No effect. We've noticed memory is a bit low,

             total       used       free     shared    buffers     cached
Mem:       3924572    3738124     186448          0    1948260     948328

but there's no swapping, so I don't really think that's the problem. We'll increase it in the VM next week to be sure.

I still get the same error messages in the Apache log trying the samples.

Any other suggestions where to look?

Scott, I'm not sure which link got you to your NaN URL, I haven't been able to reproduce that. Can you give me more detail?

  --Bob

On 10/4/13 1:31 PM, Bob Muller wrote:
Scott,

The track loading problem that Tanya mentioned turned out to be the fact that the / mount had completely filled up. I cleared out the apache logs and got 2GB freed, and the user was able to load. But then the hanging problems started, and presumably the NaN. Could the freezeup due to the disk-full problem have caused an issue somewhere in the temporary files that gbrowse creates? Where might I look?
  --Bob Muller

Nothing has changed in gbrowse, maybe something in the underlying db. I'll check when I have system access again.

  --Bob Muller

On Wednesday, October 2, 2013, Scott Cain wrote:
Hi Tanya,

I'm ccing this to the GBrowse mailing list, as I don't have much of an idea at the moment, and maybe somebody else will.

I've never seen something like this before.  When I navigate to 


and click on one of the examples, somewhere along the line, GBrowse converts that to a URL that looks like this:

  ...cgi-bin/gb2/gbrowse/arabidopsis/?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false

That NaN (Not a Number) business has be concerned that something weird is going on (a fear strengthened by the fact that it results in GBrowse eventually crashing and returning a 500 error).

So what has changed between last week and this?

Scott



On Wed, Oct 2, 2013 at 10:15 AM, Tanya Berardini <[hidden email]> wrote:
Hi Scott,

I'm back!  As you may recall, last week, we (TAIR) has some problems with our GBrowse installation not displaying custom tracks.  After some troubleshooting, we figured out that there was a problem with not enough space for files - resolved that.  However, now we've got another, bigger issue which may or may not be related to the custom track one.  While GBrowse loads up, there are no data displayed in any of the tracks!

For example:


Nice GBrowse background, no data in tracks.  I've been able to replicate this behavior on multiple computers and on multiple browsers.  This started happening mid last week.

Bob tracked down the apache errorlogs and gave me this:
----------------------------
Checked the server, no obvious problems. Each of these queries gets the same set of errors:

[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] RUN(): POST: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 239., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] session id = 5f6ff169051467103129ce0ceebc477b at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 243., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 272., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] [5659] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 275., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2818., referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[Tue Oct 01 16:49:51 2013] [error] [client 171.66.71.53] Premature end of script headers: gbrowse, referer:http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040

I do not know whether these errors have anything to do with the problem. Queries that succeeded on Friday got these same errors.
------------------

Does the data from the error logs trigger anything in your mind that might help us resolve the problem?  Any help is much appreciated.

Thanks very much,

Tanya


Tanya Berardini
TAIR Curator
www.arabidopsis.org

================
There's a new plan to sustain TAIR!  Read more at: http://bit.ly/1cCtwRV
================



--
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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


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Re: GBrowse visualization problem

Bob Muller-2
In reply to this post by Bob Muller
While attempting another debugging session in Firefox, I tried setting track preferences to make the two browser displays identical for debugging purposes.

On my Chrome GBrowse, I can set the tracks fine. On Firefox, I set the tracks, but after a few seconds, all the checks that I put in disappear. In the browser log, there's the following:

[06:41:09.145] "?action=set_favorite&label=tDNAs&favorite=1"
[06:41:10.143] POST http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ [HTTP/1.1 200 1377ms]
[06:41:10.088] "?action=update_sections&section_names=tracks_panel"
[06:41:10.537] POST http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040 [HTTP/1.1 204 No Content 1007ms]
[06:41:10.480] "?action=set_favorite&label=Polymorphism&favorite=1"
[06:41:11.540] "?action=update_sections&section_names=tracks_panel"
[06:41:11.680] POST http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ [HTTP/1.1 200 1663ms]

The update_sections parameter is the point at which the preference checks disappear.

Does anyone have an experience like this with setting preferences? Is there something amiss with the above sequence? Why are the check marks disappearing?

I also did an Inspect on the last POST:


Request URL: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
Request Method: POST
Status Code: HTTP/1.1 200
Request Headers 06:41:11.000
X-Requested-With: XMLHttpRequest
X-Prototype-Version: 1.7
User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:24.0) Gecko/20100101 Firefox/24.0
Referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
Pragma: no-cache
Host: gbrowse.tacc.utexas.edu
Content-Type: application/x-www-form-urlencoded; charset=UTF-8
Content-Length: 49
Connection: keep-alive
Cache-Control: no-cache
Accept-Language: en-US,en;q=0.5
Accept-Encoding: gzip, deflate
Accept: text/javascript, text/html, application/xml, text/xml, */*
Sent Cookie
gbrowse_sess: 5f6ff169051467103129ce0ceebc477b
__utmz: 148142433.1381246390.8.7.utmccn=(referral)|utmcsr=arabidopsis.org|utmcct=/|utmcmd=referral
__utma: 148142433.1852201754.1380233468.1381241346.1381246390.8
Response Headers Δ1399ms
Transfer-Encoding: chunked
Server: Apache/2.2.15 (CentOS)
Date: Sun, 13 Oct 2013 13:41:11 GMT
Content-Type: application/json; charset=ISO-8859-1
Connection: close
Cache-Control: no-cache
Received Cookie
gbrowse_sess: 5f6ff169051467103129ce0ceebc477b

The referer is the search in the Browser tab.

I also redid that search, it's just a click on the Example AT1G01040, and got this in the console:

[06:54:05.460] GET http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040 [HTTP/1.1 200 OK 1956ms]
[06:54:07.197] Error in parsing value for 'padding-top'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/tracks.css:3
[06:54:07.197] Error in parsing value for 'padding-bottom'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/tracks.css:4
[06:54:07.199] Error in parsing value for 'filter'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/karyotype.css:5
[06:54:07.199] Error in parsing value for 'filter'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/karyotype.css:15
[06:54:07.200] Unknown property 'zoom'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/dropdown/dropdown.css:37
[06:54:07.221] Selector expected. Ruleset ignored due to bad selector. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/gbrowse.css:131
[06:54:07.466] Expected ':' but found ';'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[06:54:07.696] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/d55cbc4b6a826700a753f5a998235770.png [HTTP/1.1 200 OK 65ms]
[06:54:07.697] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/a7dc0c4aa4797a3dc02f1d1cb2bdd063.png [HTTP/1.1 200 OK 65ms]
[06:54:07.698] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/3220c386dd715d50c933cb6540197be7.png [HTTP/1.1 200 OK 66ms]
[06:54:07.700] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/532f485a6b8777dcff2512cee1e95c39.png [HTTP/1.1 200 OK 67ms]
[06:54:07.701] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/55d8d327ccccf350e92d74dd4462ae71.png [HTTP/1.1 200 OK 67ms]
[06:54:07.702] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/1265f4dd2ff4367820eccf4b66978f60.png [HTTP/1.1 200 OK 126ms]
[06:54:07.890] "?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false"
[06:54:08.067] POST http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ [HTTP/1.1 500 Internal Server Error 886ms]

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Re: GBrowse visualization problem

Bob Muller
In reply to this post by Bob Muller
While attempting another debugging session in Firefox, I tried setting track preferences to make the two browser displays identical for debugging purposes.

On my Chrome GBrowse, I can set the tracks fine. On Firefox, I set the tracks, but after a few seconds, all the checks that I put in disappear. In the browser log, there's the following:

[06:41:09.145] "?action=set_favorite&label=tDNAs&favorite=1"
[06:41:10.143] POST http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ [HTTP/1.1 200 1377ms]
[06:41:10.088] "?action=update_sections&section_names=tracks_panel"
[06:41:10.537] POST http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040 [HTTP/1.1 204 No Content 1007ms]
[06:41:10.480] "?action=set_favorite&label=Polymorphism&favorite=1"
[06:41:11.540] "?action=update_sections&section_names=tracks_panel"
[06:41:11.680] POST http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ [HTTP/1.1 200 1663ms]

The update_sections parameter is the point at which the preference checks disappear.

Does anyone have an experience like this with setting preferences? Is there something amiss with the above sequence? Why are the check marks disappearing?

I also did an Inspect on the last POST:


Request URL: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/
Request Method: POST
Status Code: HTTP/1.1 200
Request Headers 06:41:11.000
X-Requested-With: XMLHttpRequest
X-Prototype-Version: 1.7
User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:24.0) Gecko/20100101 Firefox/24.0
Referer: http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
Pragma: no-cache
Host: gbrowse.tacc.utexas.edu
Content-Type: application/x-www-form-urlencoded; charset=UTF-8
Content-Length: 49
Connection: keep-alive
Cache-Control: no-cache
Accept-Language: en-US,en;q=0.5
Accept-Encoding: gzip, deflate
Accept: text/javascript, text/html, application/xml, text/xml, */*
Sent Cookie
gbrowse_sess: 5f6ff169051467103129ce0ceebc477b
__utmz: 148142433.1381246390.8.7.utmccn=(referral)|utmcsr=arabidopsis.org|utmcct=/|utmcmd=referral
__utma: 148142433.1852201754.1380233468.1381241346.1381246390.8
Response Headers Δ1399ms
Transfer-Encoding: chunked
Server: Apache/2.2.15 (CentOS)
Date: Sun, 13 Oct 2013 13:41:11 GMT
Content-Type: application/json; charset=ISO-8859-1
Connection: close
Cache-Control: no-cache
Received Cookie
gbrowse_sess: 5f6ff169051467103129ce0ceebc477b

The referer is the search in the Browser tab.

I also redid that search, it's just a click on the Example AT1G01040, and got this in the console:

[06:54:05.460] GET http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040 [HTTP/1.1 200 OK 1956ms]
[06:54:07.197] Error in parsing value for 'padding-top'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/tracks.css:3
[06:54:07.197] Error in parsing value for 'padding-bottom'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/tracks.css:4
[06:54:07.199] Error in parsing value for 'filter'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/karyotype.css:5
[06:54:07.199] Error in parsing value for 'filter'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/karyotype.css:15
[06:54:07.200] Unknown property 'zoom'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/dropdown/dropdown.css:37
[06:54:07.221] Selector expected. Ruleset ignored due to bad selector. @ http://gbrowse.tacc.utexas.edu/gbrowse2/css/gbrowse.css:131
[06:54:07.466] Expected ':' but found ';'. Declaration dropped. @ http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/?name=AT1G01040
[06:54:07.696] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/d55cbc4b6a826700a753f5a998235770.png [HTTP/1.1 200 OK 65ms]
[06:54:07.697] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/a7dc0c4aa4797a3dc02f1d1cb2bdd063.png [HTTP/1.1 200 OK 65ms]
[06:54:07.698] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/3220c386dd715d50c933cb6540197be7.png [HTTP/1.1 200 OK 66ms]
[06:54:07.700] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/532f485a6b8777dcff2512cee1e95c39.png [HTTP/1.1 200 OK 67ms]
[06:54:07.701] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/55d8d327ccccf350e92d74dd4462ae71.png [HTTP/1.1 200 OK 67ms]
[06:54:07.702] GET http://gbrowse.tacc.utexas.edu/gbrowse2/i/arabidopsis/1265f4dd2ff4367820eccf4b66978f60.png [HTTP/1.1 200 OK 126ms]
[06:54:07.890] "?action=navigate&navigate=left%200&view_start=NaN&view_stop=NaN&snapshot=false"
[06:54:08.067] POST http://gbrowse.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ [HTTP/1.1 500 Internal Server Error 886ms]

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October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk
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