Database Not Found

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Database Not Found

Matthew Johnson
Hello everyone,

I have loaded a databased into gbrowse called “draft2”.  When I navigate to it, gbrowse doesn’t show anything and I get a “Not Found” in red letters.  After reading of a similar issue online, I gave RWX privileges to all users to my gbrowse2, databases, and draft2 directory located at /var/lib/gbrowse2/databases/draft2.  I didn’t change privileges in my /var/lib/ directory.  When I navigate to the draft2 database from gbrowse, apache says: 

[Tue May 27 08:57:31 2014] [error] [client ::1] , referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] MSG: No suitable files found in /var/lib/gbrowse2/databases/draft2/, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Error::throw, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::Root::Root::throw /Library/Perl/5.16/Bio/Root/Root.pm:486, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::IndexedBase::index_dir /Library/Perl/5.16/Bio/DB/IndexedBase.pm:444, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::IndexedBase::new /Library/Perl/5.16/Bio/DB/IndexedBase.pm:361, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::memory::commit /Library/Perl/5.16/Bio/DB/SeqFeature/Store/memory.pm:172, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /Library/Perl/5.16/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /Library/Perl/5.16/Bio/DB/SeqFeature/Store/Loader.pm:354, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::Loader::load /Library/Perl/5.16/Bio/DB/SeqFeature/Store/Loader.pm:243, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::memory::post_init /Library/Perl/5.16/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::new /Library/Perl/5.16/Bio/DB/SeqFeature/Store.pm:395, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::Graphics::Browser2::DataBase::open_database /Library/Perl/5.16/darwin-thread-multi-2level/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::Graphics::Browser2::DataSource::open_database /Library/Perl/5.16/darwin-thread-multi-2level/Bio/Graphics/Browser2/DataSource.pm:997, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::Graphics::Browser2::Render::init_database /Library/Perl/5.16/darwin-thread-multi-2level/Bio/Graphics/Browser2/Render.pm:1086, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::Graphics::Browser2::Render::init /Library/Perl/5.16/darwin-thread-multi-2level/Bio/Graphics/Browser2/Render.pm:345, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: GBrowse_img::run /Library/WebServer/CGI-Executables/gb2/gbrowse_img:108, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: /Library/WebServer/CGI-Executables/gb2/gbrowse_img:69, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] -----------------------------------------------------------, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] Can't call method "seq_id" on an undefined value at /Library/Perl/5.16/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] Premature end of script headers: gbrowse_img, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/


So it seems that apache cannot find suitable files located in the /var/lib/gbrowse2/databases/draft2/ directory. so I ran $ ls /var/lib/gbrowse2/databses/draft2 and it gave me:
draft2.gff3

I also ran $ ls -al /var/lib/gbrowse2/databases/draft2 and that gave me:
total 24
drwxrwxrwx   4 biosci  _www    136 May  2 13:16 .
drwxrwxrwx  12 biosci  _www    408 May  1 15:47 ..
-rw-r--r--@  1 biosci  _www   6148 May  1 15:50 .DS_Store
-rwxrwxrwx@  1 biosci  staff   569 May  2 13:16 draft2.gff3

Although, I was thinking the problem isn’t about suitable files being in the right location because when I navigate to the sample yeast database, it shows up fine in gbrowse (to my knowledge) yet apache gives the same lines of messages (MSG: No suitable files found in /opt/local/apache2/htdocs/gbrowse2/databases/yeast_chr1+2) minus the “Can’t call method seq_id” like it says with my draft2 database.  Could it be problems with the “seq_id"?

Here is my draft2.gff file

##gff-version 3
ch1-1 FGenesh++ CDS 1159 1863 92.55 - 0 .
ch1-1 FGenesh++ CDS 2166 2176 34.3 + 0 .
ch1-1 FGenesh++ CDS 2564 2651 145.96 + 1 .
ch1-1 FGenesh++ CDS 2763 3532 716.94 + 0 .
ch1-1 FGenesh++ CDS 3729 3798 138.31 + 1 .
ch1-1 FGenesh++ CDS 4895 4983 83.72 + 0 .
ch1-1 FGenesh++ CDS 5068 5101 10 . 0 .
ch1-1 FGenesh++ CDS 5839 6117 468.52 - 0 .
ch1-1 FGenesh++ CDS 6334 6387 113.05 - 0 .
ch1-1 FGenesh++ CDS 6476 6536 97.03 - 1 .
ch1-1 FGenesh++ CDS 6710 6768 97.78 - 0 .
ch1-1 FGenesh++ CDS 6861 6929 106.14 - 0 .
ch1-1 FGenesh++ CDS 7106 7378 367.98 - 0 .

Here is the top of my draft2.conf file (copied conf file from volvox and altered for my draft2 database)

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
-dir /var/lib/gbrowse2/databases/draft2/

Here is the RenderPanels.pm file (line 2058-2081)

my @argv = (
      -grid         => $section eq 'detail' ? $settings->{'grid'} : 0,
              -seqid        => $segment->seq_id,
      -start        => $seg_start,
      -end          => $seg_stop,
      -stop         => $seg_stop,  #backward compatibility with old bioperl
      -key_color    => $source->global_setting('key bgcolor')      || 'moccasin',
      -bgcolor      => $source->global_setting("$section bgcolor") || 'wheat',
              -width        => $section eq 'detail'? $self->get_detail_width_no_pad : $settings->{width},
      -key_style    => $keystyle,
              -suppress_key => 1,
      -empty_tracks => $source->global_setting('empty_tracks')    || DEFAULT_EMPTYTRACKS,
      -pad_top      => $image_class->gdMediumBoldFont->height+2,
              -pad_bottom   => 3,
      -image_class  => $image_class,
      -postgrid     => $postgrid,
      -background   => $args->{background} || '',
      -truecolor    => $source->global_setting('truecolor') || 0,
      -map_fonts_to_truetype    => $source->global_setting('truetype') || 0,
      -extend_grid  => 1,
              -gridcolor    => $source->global_setting('grid color') || 'lightcyan',
              -gridmajorcolor    => $source->global_setting('grid major color') || 'cyan',
      @pass_thru_args,   # position is important here to allow user to override settings
    );


I would greatly appreciate any feedback.

Thanks,
Matt

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Re: Database Not Found

Scott Cain
Hi Matt,

Thanks for the thorough error report.  I believe you're being bitten by a bug in the current release of BioPerl.  Probably the best way to fix this is to revert to an older version of Bioperl:


If you don't want to do that, I think a workaround is move your fasta data into a separate file, but just remember that you may get bitten by this again.  I don't think there is a downside to using the older BioPerl with regards to using GBrowse (obviously, with other parts of BioPerl you'd have to check what changed).

Scott



On Sun, Jun 1, 2014 at 11:56 AM, Matthew Johnson <[hidden email]> wrote:
Hello everyone,

I have loaded a databased into gbrowse called “draft2”.  When I navigate to it, gbrowse doesn’t show anything and I get a “Not Found” in red letters.  After reading of a similar issue online, I gave RWX privileges to all users to my gbrowse2, databases, and draft2 directory located at /var/lib/gbrowse2/databases/draft2.  I didn’t change privileges in my /var/lib/ directory.  When I navigate to the draft2 database from gbrowse, apache says: 

[Tue May 27 08:57:31 2014] [error] [client ::1] , referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] MSG: No suitable files found in /var/lib/gbrowse2/databases/draft2/, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Error::throw, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::Root::Root::throw /Library/Perl/5.16/Bio/Root/Root.pm:486, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::IndexedBase::index_dir /Library/Perl/5.16/Bio/DB/IndexedBase.pm:444, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::IndexedBase::new /Library/Perl/5.16/Bio/DB/IndexedBase.pm:361, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::memory::commit /Library/Perl/5.16/Bio/DB/SeqFeature/Store/memory.pm:172, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /Library/Perl/5.16/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /Library/Perl/5.16/Bio/DB/SeqFeature/Store/Loader.pm:354, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::Loader::load /Library/Perl/5.16/Bio/DB/SeqFeature/Store/Loader.pm:243, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::memory::post_init /Library/Perl/5.16/Bio/DB/SeqFeature/Store/memory.pm:164, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::DB::SeqFeature::Store::new /Library/Perl/5.16/Bio/DB/SeqFeature/Store.pm:395, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::Graphics::Browser2::DataBase::open_database /Library/Perl/5.16/darwin-thread-multi-2level/Bio/Graphics/Browser2/DataBase.pm:44, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::Graphics::Browser2::DataSource::open_database /Library/Perl/5.16/darwin-thread-multi-2level/Bio/Graphics/Browser2/DataSource.pm:997, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::Graphics::Browser2::Render::init_database /Library/Perl/5.16/darwin-thread-multi-2level/Bio/Graphics/Browser2/Render.pm:1086, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: Bio::Graphics::Browser2::Render::init /Library/Perl/5.16/darwin-thread-multi-2level/Bio/Graphics/Browser2/Render.pm:345, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: GBrowse_img::run /Library/WebServer/CGI-Executables/gb2/gbrowse_img:108, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] STACK: /Library/WebServer/CGI-Executables/gb2/gbrowse_img:69, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] -----------------------------------------------------------, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] Can't call method "seq_id" on an undefined value at /Library/Perl/5.16/darwin-thread-multi-2level/Bio/Graphics/Browser2/RenderPanels.pm line 2058., referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/
[Tue May 27 08:57:31 2014] [error] [client ::1] Premature end of script headers: gbrowse_img, referer: http://localhost/cgi-bin/gb2/gbrowse/draft2/


So it seems that apache cannot find suitable files located in the /var/lib/gbrowse2/databases/draft2/ directory. so I ran $ ls /var/lib/gbrowse2/databses/draft2 and it gave me:
draft2.gff3

I also ran $ ls -al /var/lib/gbrowse2/databases/draft2 and that gave me:
total 24
drwxrwxrwx   4 biosci  _www    136 May  2 13:16 .
drwxrwxrwx  12 biosci  _www    408 May  1 15:47 ..
-rw-r--r--@  1 biosci  _www   6148 May  1 15:50 .DS_Store
-rwxrwxrwx@  1 biosci  staff   569 May  2 13:16 draft2.gff3

Although, I was thinking the problem isn’t about suitable files being in the right location because when I navigate to the sample yeast database, it shows up fine in gbrowse (to my knowledge) yet apache gives the same lines of messages (MSG: No suitable files found in /opt/local/apache2/htdocs/gbrowse2/databases/yeast_chr1+2) minus the “Can’t call method seq_id” like it says with my draft2 database.  Could it be problems with the “seq_id"?

Here is my draft2.gff file

##gff-version 3
ch1-1 FGenesh++ CDS 1159 1863 92.55 - 0 .
ch1-1 FGenesh++ CDS 2166 2176 34.3 + 0 .
ch1-1 FGenesh++ CDS 2564 2651 145.96 + 1 .
ch1-1 FGenesh++ CDS 2763 3532 716.94 + 0 .
ch1-1 FGenesh++ CDS 3729 3798 138.31 + 1 .
ch1-1 FGenesh++ CDS 4895 4983 83.72 + 0 .
ch1-1 FGenesh++ CDS 5068 5101 10 . 0 .
ch1-1 FGenesh++ CDS 5839 6117 468.52 - 0 .
ch1-1 FGenesh++ CDS 6334 6387 113.05 - 0 .
ch1-1 FGenesh++ CDS 6476 6536 97.03 - 1 .
ch1-1 FGenesh++ CDS 6710 6768 97.78 - 0 .
ch1-1 FGenesh++ CDS 6861 6929 106.14 - 0 .
ch1-1 FGenesh++ CDS 7106 7378 367.98 - 0 .

Here is the top of my draft2.conf file (copied conf file from volvox and altered for my draft2 database)

[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
-dir /var/lib/gbrowse2/databases/draft2/

Here is the RenderPanels.pm file (line 2058-2081)

my @argv = (
      -grid         => $section eq 'detail' ? $settings->{'grid'} : 0,
              -seqid        => $segment->seq_id,
      -start        => $seg_start,
      -end          => $seg_stop,
      -stop         => $seg_stop,  #backward compatibility with old bioperl
      -key_color    => $source->global_setting('key bgcolor')      || 'moccasin',
      -bgcolor      => $source->global_setting("$section bgcolor") || 'wheat',
              -width        => $section eq 'detail'? $self->get_detail_width_no_pad : $settings->{width},
      -key_style    => $keystyle,
              -suppress_key => 1,
      -empty_tracks => $source->global_setting('empty_tracks')    || DEFAULT_EMPTYTRACKS,
      -pad_top      => $image_class->gdMediumBoldFont->height+2,
              -pad_bottom   => 3,
      -image_class  => $image_class,
      -postgrid     => $postgrid,
      -background   => $args->{background} || '',
      -truecolor    => $source->global_setting('truecolor') || 0,
      -map_fonts_to_truetype    => $source->global_setting('truetype') || 0,
      -extend_grid  => 1,
              -gridcolor    => $source->global_setting('grid color') || 'lightcyan',
              -gridmajorcolor    => $source->global_setting('grid major color') || 'cyan',
      @pass_thru_args,   # position is important here to allow user to override settings
    );


I would greatly appreciate any feedback.

Thanks,
Matt

------------------------------------------------------------------------------
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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