Features not shown on tutorial for volvox

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Features not shown on tutorial for volvox

gtoth
We’ve installed gbrowse 2 and its prerequisites on rhel 6.  When we go to
http://localhost/cgi-bin/gb2/gbrowse/volvox and enter ctgA in Search we get
the Overview, Region and Details lines, but no features are shown.  The
error_log contains the following:

[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] , referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] -------------
EXCEPTION: Bio::Root::Exception -------------, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] MSG: No suitable
files found in /var/lib/gbrowse2/databases/volvox, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Error::throw, referer: http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::DB::IndexedBase::index_dir
/usr/local/share/perl5/Bio/DB/IndexedBase.pm:444, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::DB::IndexedBase::new /usr/local/share/perl5/Bio/DB/IndexedBase.pm:361,
referer: http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::DB::SeqFeature::Store::memory::commit
/usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:172, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::DB::SeqFeature::Store::GFF3Loader::finish_load
/usr/local/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::DB::SeqFeature::Store::Loader::load_fh
/usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::DB::SeqFeature::Store::Loader::load
/usr/local/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::DB::SeqFeature::Store::memory::post_init
/usr/local/share/perl5/Bio/DB/SeqFeature/Store/memory.pm:164, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::DB::SeqFeature::Store::new
/usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:395, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::Graphics::Browser2::DataBase::open_database
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm:44, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::Graphics::Browser2::DataSource::open_database
/usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm:997, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::Graphics::Browser2::Render::init_database
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:1088, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::Graphics::Browser2::Render::init
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:346, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
Bio::Graphics::Browser2::Render::run
/usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm:288, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83] STACK:
/var/www/cgi-bin/gb2/gbrowse:54, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/
[Wed Feb 26 08:21:22 2014] [error] [client 204.47.172.83]
-----------------------------------------------------------, referer:
http://localhost/cgi-bin/gb2/gbrowse/volvox/

A very similar posting was made to gmod-gbrowse: Dec 09, 2013; 1:51am  
error for test page

The ownerships were changed to follow the responses to that posting, but
features are still not shown.

a) httpd running as apache
b) /var/lib/gbrowse2 owned by apache
c) /var and /var/lib read and execute ok for all
d) file volvox_remarks.gff3 is there (can be opened from within the
tutorial)
e) same issue with yeast_chr1+2, so doubt file corruption
f) context set to unconfined_u:object_r:httpd_sys_rw_content_t:s0 for
/var/lib/gbrowse2 and everything below.

Thanks for any responses

Greg



--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Features-not-shown-on-tutorial-for-volvox-tp5712292.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse