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Genome Browser 2 can't find the gene fragment
Hi!
I tried to put the genome on GBrowser2.
Prerequisites of installing GBrowser2 had been confirmed.
Then I put the file of gff, DNA Sequence(.fa), and summary.gff(made of .fa file) into the directory "/var/lib/gbrowse2/databases/xxx".
Being displayed well of them which I'd tried is only the genome of Volvox.
I can search its sequence by inputting the name of the sequnce.
Other genome are failed to be searched.
Key in the name from .fa file and see that it can't find the sequnce.
Why?
I've read the error log and got the error message below.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] RUN(): GET: http://iii.iii.iii.iii/cgi-bin/gb2/g...Chlorella_New/ at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] session id = f69ba29d1e69f629493c8971602f9a74 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 273.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 287.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 290.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] render() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 297.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] 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.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] cleanup at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 301.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] session flush at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 305.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] synchronous exit at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 310.
thx
I tried to put the genome on GBrowser2.
Prerequisites of installing GBrowser2 had been confirmed.
Then I put the file of gff, DNA Sequence(.fa), and summary.gff(made of .fa file) into the directory "/var/lib/gbrowse2/databases/xxx".
Being displayed well of them which I'd tried is only the genome of Volvox.
I can search its sequence by inputting the name of the sequnce.
Other genome are failed to be searched.
Key in the name from .fa file and see that it can't find the sequnce.
Why?
I've read the error log and got the error message below.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] RUN(): GET: http://iii.iii.iii.iii/cgi-bin/gb2/g...Chlorella_New/ at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] session id = f69ba29d1e69f629493c8971602f9a74 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 273.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 287.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 290.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] render() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 297.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] 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.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] cleanup at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 301.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] session flush at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 305.
[Mon Sep 22 15:52:02 2014] [error] [client xxx.xxx.xxx.xxx] [23493] synchronous exit at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 310.
thx