GBrowse 500 internal server error

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GBrowse 500 internal server error

John Portwood
Hello,

We have GBrowse installed on a server running CentOS 6.5, and haven't had any issues until earlier today. I tried to load a very large track into an SQLite database with the bp_seqfeature_load script, but this eventually consumed all of the available disk space in the /tmp folder. I deleted a very large file in the /tmp directory with a name like "feature.00000" (where 00000 was some random #) to immediately free up space. When I checked GBrowse afterwards, it was working fine in Chrome but not Firefox, IE, or Safari. I tried restarting apache and running the gbrowse_clean.pl script, and somehow or another I managed to break it in Chrome too... 

The browser is currently reporting a 500 server error when making a POST request in the prototype.js file. 

POST http://gblade.usda.iastate.edu/gb2/gbrowse/maize_v4/ 500 (Internal Server Error)

The apache error logs from the GET request are reporting:

[Tue Jun 27 16:22:40 2017] [error] [client 10.24.27.217] [33669] RUN(): GET: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/  at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240.
[Tue Jun 27 16:22:40 2017] [error] [client 10.24.27.217] [33669] session id = 6f249cdfda49986a1f48c2c1912d1949 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244.
[Tue Jun 27 16:22:40 2017] [error] [client 10.24.27.217] [33669] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 273.
[Tue Jun 27 16:22:40 2017] [error] [client 10.24.27.217] [33669] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276.
[Tue Jun 27 16:22:40 2017] [error] [client 10.24.27.217] [33669] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 287.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] [33669] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 290.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] [33669] render() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 297.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] GBROWSE NOTICE: To enable PDF generation, please enter the directory "/var/www" and run the commands: "sudo mkdir -p .config/inkscape .gnome2" and "sudo chown apache .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] [33669] cleanup at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 301.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] [33669] session flush at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 305.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] [33669] synchronous exit at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 310.
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] [33671] RUN(): POST: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] [33671] session id = 94513a0906ccb097664c62a24f809e82 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] [33671] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 273., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] [33671] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2860., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2916., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2095., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Premature end of script headers: gbrowse, referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/

I suspect the issue is with the view_start=NaN;view_end=NaN parameters in the POST request (highlighted above). Does anyone have any advice about what could be causing this issue?
--
Thanks,
John Portwood
1028 Crop Genome Informatics Laboratory 
Iowa State University - USDA - ARS
Ames, IA 50010

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Re: GBrowse 500 internal server error

John Portwood
Hi all,

This issue has been resolved with the help of Nathan Weeks! It turns out the session database located in /var/lib/gbrowse2/sessions/ had become corrupted when the file system temporarily filled up. Renaming the databases cgisesss.db and cgisess.db.lck to force apache to recreate them resolved the NaN issue. 

Thanks,
John 

On Tue, Jun 27, 2017 at 4:32 PM, John Portwood <[hidden email]> wrote:
Hello,

We have GBrowse installed on a server running CentOS 6.5, and haven't had any issues until earlier today. I tried to load a very large track into an SQLite database with the bp_seqfeature_load script, but this eventually consumed all of the available disk space in the /tmp folder. I deleted a very large file in the /tmp directory with a name like "feature.00000" (where 00000 was some random #) to immediately free up space. When I checked GBrowse afterwards, it was working fine in Chrome but not Firefox, IE, or Safari. I tried restarting apache and running the gbrowse_clean.pl script, and somehow or another I managed to break it in Chrome too... 

The browser is currently reporting a 500 server error when making a POST request in the prototype.js file. 

POST http://gblade.usda.iastate.edu/gb2/gbrowse/maize_v4/ 500 (Internal Server Error)

The apache error logs from the GET request are reporting:

[Tue Jun 27 16:22:40 2017] [error] [client 10.24.27.217] [33669] RUN(): GET: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/  at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240.
[Tue Jun 27 16:22:40 2017] [error] [client 10.24.27.217] [33669] session id = 6f249cdfda49986a1f48c2c1912d1949 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244.
[Tue Jun 27 16:22:40 2017] [error] [client 10.24.27.217] [33669] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 273.
[Tue Jun 27 16:22:40 2017] [error] [client 10.24.27.217] [33669] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276.
[Tue Jun 27 16:22:40 2017] [error] [client 10.24.27.217] [33669] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 287.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] [33669] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 290.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] [33669] render() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 297.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] GBROWSE NOTICE: To enable PDF generation, please enter the directory "/var/www" and run the commands: "sudo mkdir -p .config/inkscape .gnome2" and "sudo chown apache .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] [33669] cleanup at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 301.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] [33669] session flush at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 305.
[Tue Jun 27 16:22:41 2017] [error] [client 10.24.27.217] [33669] synchronous exit at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 310.
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] [33671] RUN(): POST: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/ action=navigate;navigate=left%200;view_start=NaN;view_stop=NaN;snapshot=false at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] [33671] session id = 94513a0906ccb097664c62a24f809e82 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] [33671] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 273., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] [33671] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2860., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Use of uninitialized value in concatenation (.) or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 2916., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Can't call method "seq_id" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2095., referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/
[Tue Jun 27 16:22:42 2017] [error] [client 10.24.27.217] Premature end of script headers: gbrowse, referer: http://gblade.usda.iastate.edu/gb2/gbrowse/maize_ph207/

I suspect the issue is with the view_start=NaN;view_end=NaN parameters in the POST request (highlighted above). Does anyone have any advice about what could be causing this issue?
--
Thanks,
John Portwood
1028 Crop Genome Informatics Laboratory 
Iowa State University - USDA - ARS
Ames, IA 50010



--
Thanks,
John Portwood
1028 Crop Genome Informatics Laboratory 
Iowa State University - USDA - ARS
Ames, IA 50010

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