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Old 09-24-2014, 06:40 AM   #1
Junior Member
Location: Taiwan, Asia

Join Date: Sep 2014
Posts: 2
Question Genome Browser 2 can't find the gene fragment

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.

I've read the error log and got the error message below.

[Mon Sep 22 15:52:02 2014] [error] [client] [23493] RUN(): GET: http://iii.iii.iii.iii/cgi-bin/gb2/g...Chlorella_New/ at /usr/local/lib64/perl5/Bio/Graphics/Browser2/ line 240.
[Mon Sep 22 15:52:02 2014] [error] [client] [23493] session id = f69ba29d1e69f629493c8971602f9a74 at /usr/local/lib64/perl5/Bio/Graphics/Browser2/ line 244.
[Mon Sep 22 15:52:02 2014] [error] [client] [23493] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/ line 273.
[Mon Sep 22 15:52:02 2014] [error] [client] [23493] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/ line 276.
[Mon Sep 22 15:52:02 2014] [error] [client] [23493] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/ line 287.
[Mon Sep 22 15:52:02 2014] [error] [client] [23493] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/ line 290.
[Mon Sep 22 15:52:02 2014] [error] [client] [23493] render() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/ line 297.
[Mon Sep 22 15:52:02 2014] [error] [client] 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] [23493] cleanup at /usr/local/lib64/perl5/Bio/Graphics/Browser2/ line 301.
[Mon Sep 22 15:52:02 2014] [error] [client] [23493] session flush at /usr/local/lib64/perl5/Bio/Graphics/Browser2/ line 305.
[Mon Sep 22 15:52:02 2014] [error] [client] [23493] synchronous exit at /usr/local/lib64/perl5/Bio/Graphics/Browser2/ line 310.

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