gbrowse install errors

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gbrowse install errors

xiongjie
Hi, all

I have installed the gbrowse2 in a redhat server.
Now I can access the test yeast page, but it can not show correctly.

I checked the apache error_log file, like bellow, how can I fix this problem? Thanks.
内嵌图片 1

[Mon Jan 12 10:27:06.332038 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: , referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.332167 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://
[Mon Jan 12 10:27:06.332255 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: MSG: No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2, ref
[Mon Jan 12 10:27:06.332284 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Error::throw, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_a
dvanced/?name=chrI
[Mon Jan 12 10:27:06.332371 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486, re
[Mon Jan 12 10:27:06.332474 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::IndexedBase::index_dir /usr/local/share/perl5/Bio/DB/IndexedB
[Mon Jan 12 10:27:06.332569 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::IndexedBase::new /usr/local/share/perl5/Bio/DB/IndexedBase.pm
[Mon Jan 12 10:27:06.332745 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::memory::commit /usr/local/share/perl5/Bio/
[Mon Jan 12 10:27:06.332940 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/share/p
erl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.333070 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl5/Bio
/DB/SeqFeature/Store/Loader.pm:354, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.333195 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB
[Mon Jan 12 10:27:06.333325 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/B
[Mon Jan 12 10:27:06.333433 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeatu
[Mon Jan 12 10:27:06.333566 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl
5/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.333713 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/pe
rl5/Bio/Graphics/Browser2/DataSource.pm:997, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.333872 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/lo
cal/lib64/perl5/Bio/Graphics/Browser2/RegionSearch.pm:403, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.334016 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib6
4/perl5/Bio/Graphics/Browser2/RegionSearch.pm:301, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.334139 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib64/perl5/Bio/Gra
[Mon Jan 12 10:27:06.334263 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib64/perl5/Bio/Gr
[Mon Jan 12 10:27:06.334393 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib64/perl5/
Bio/Graphics/Browser2/Render.pm:1940, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.334523 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib64/perl5/B
io/Graphics/Browser2/Render.pm:1930, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.334641 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphi
[Mon Jan 12 10:27:06.334699 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: STACK: /var/www/cgi-bin/gb2/gbrowse:54, referer: http://172.20.26.72/cgi-bin/
gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:06.334786 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: -----------------------------------------------------------, referer: http://
[Mon Jan 12 10:27:06.438501 2015] [cgi:error] [pid 37361] [client 10.21.211.40:58422] AH01215: GBROWSE NOTICE: To enable PDF generation, please enter the directory "/usr/sh
are/httpd" 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., referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=chrI
[Mon Jan 12 10:27:07.802577 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: GBROWSE NOTICE: To enable PDF generation, please enter the directory "/usr/sh
are/httpd" 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., referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.416004 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: , referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membr
ane%20trafficking
[Mon Jan 12 10:27:08.416134 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://
[Mon Jan 12 10:27:08.416222 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: MSG: No suitable files found in /var/lib/gbrowse2/databases/yeast_chr1+2, ref
[Mon Jan 12 10:27:08.416252 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Error::throw, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_a
dvanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.416338 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486, re
[Mon Jan 12 10:27:08.416440 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::IndexedBase::index_dir /usr/local/share/perl5/Bio/DB/IndexedB
[Mon Jan 12 10:27:08.416536 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::IndexedBase::new /usr/local/share/perl5/Bio/DB/IndexedBase.pm
[Mon Jan 12 10:27:08.416663 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::memory::commit /usr/local/share/perl5/Bio/
[Mon Jan 12 10:27:08.416830 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/local/share/p
erl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.416965 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/local/share/perl5/Bio
[Mon Jan 12 10:27:08.417090 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/local/share/perl5/Bio/DB
[Mon Jan 12 10:27:08.417246 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/local/share/perl5/B
[Mon Jan 12 10:27:08.417355 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::DB::SeqFeature::Store::new /usr/local/share/perl5/Bio/DB/SeqFeatu
[Mon Jan 12 10:27:08.417487 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/local/lib64/perl
[Mon Jan 12 10:27:08.417625 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/local/lib64/pe
[Mon Jan 12 10:27:08.417769 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::DataSource::show_summary /usr/local/lib64/per
[Mon Jan 12 10:27:08.417920 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::RenderPanels::subtrack_manager /usr/local/lib
64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:2268, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.418071 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::RenderPanels::select_features_menu /usr/local
/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:1672, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.418220 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::RenderPanels::wrap_rendered_track /usr/local/
lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm:649, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.418345 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::Render::scale_bar /usr/local/lib64/perl5/Bio/
[Mon Jan 12 10:27:08.418475 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::Render::render_panels /usr/local/lib64/perl5/
[Mon Jan 12 10:27:08.418602 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::Render::render_body /usr/local/lib64/perl5/Bi
[Mon Jan 12 10:27:08.418729 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::Render::render /usr/local/lib64/perl5/Bio/Gra
[Mon Jan 12 10:27:08.418852 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib64/perl5/Bio/Graphi
[Mon Jan 12 10:27:08.418910 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: STACK: /var/www/cgi-bin/gb2/gbrowse:54, referer: http://172.20.26.72/cgi-bin/
gb2/gbrowse/yeast_advanced/?name=membrane%20trafficking
[Mon Jan 12 10:27:08.418984 2015] [cgi:error] [pid 62642] [client 10.21.211.40:58426] AH01215: -----------------------------------------------------------, referer: http://

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