2 Problems concerning track loading/Error Message

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2 Problems concerning track loading/Error Message

Nadine Elpida Tatto
Hi there,


I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems now.http://www.pichiagenome.org/ is the site


1) Most of the time there is an error message popping up I can't figure out the reason for:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK: Bio::Graphics::Browser2::Region::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK: Bio::Graphics::Browser2::Region::lookup_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK: Bio::Graphics::Browser2::Region::search_db /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK: /usr/lib/cgi-bin/gb2/gbrowse:50


2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore


This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.


I would appreciate any hint for solving this problems





Thank you


Nadine




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Re: 2 Problems concerning track loading/Error Message

Scott Cain
Hi Nadine,

That error message isn't much to go on; that message comes from the work-horse method that does name searching in the Chado adaptor, so quite a few things could be going on.

Just to be clear--the site worked fine a few weeks ago but now does not, right?  So the question is, what changed?  Did GBrowse, BioPerl or Postgres get updated?  Was data added or deleted from the Chado database?  Was full text searching turned on with out prepping the database?

If none of these things appear to be the case, I'd suggest turning on DEBUG (locating the use constant DEBUG => 0; line and changing it to 1) in Chado.pm and trying to load a region.  That will produce an enormous amount of output in the apache error_log, and you can send that as an attachment to the list if nothing obvious jumps out at you.

Scott


On Thu, Oct 16, 2014 at 5:21 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi there,


I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems now.http://www.pichiagenome.org/ is the site


1) Most of the time there is an error message popping up I can't figure out the reason for:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK: Bio::Graphics::Browser2::Region::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK: Bio::Graphics::Browser2::Region::lookup_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK: Bio::Graphics::Browser2::Region::search_db /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK: /usr/lib/cgi-bin/gb2/gbrowse:50


2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore


This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.


I would appreciate any hint for solving this problems





Thank you


Nadine




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--
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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

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Re: 2 Problems concerning track loading/Error Message

Nadine Elpida Tatto
Dear Scott,

thats right, it worked fine some weeks ago, despite the fact that this error message occured now and then even before this complete failure, but without any effects on the function. Nevertheless it was not used so much until now, maybe this might be the reason that no one noticed that there is a problem with our installation.

I've changed nothing according the things you've mentioned.

There is an additional error message in the apache error.log:
[Thu Oct 16 14:59:07 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/ 

AND

[Thu Oct 16 14:59:07 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 14:59:07 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/

I've also noticed that the error.log got so big, that it used my complete disk. I've had to delete it. After that the browser showed at least something again, but features still can't be displayed.

I will try out what comes out with debugging set on 1 and will mail again.


Thank you for your help.




Nadine





>>> Scott Cain <[hidden email]> 10/16/14 2:38 PM >>>
Hi Nadine,

That error message isn't much to go on; that message comes from the work-horse method that does name searching in the Chado adaptor, so quite a few things could be going on.


Just to be clear--the site worked fine a few weeks ago but now does not, right?  So the question is, what changed?  Did GBrowse, BioPerl or Postgres get updated?  Was data added or deleted from the Chado database?  Was full text searching turned on with out prepping the database?


If none of these things appear to be the case, I'd suggest turning on DEBUG (locating the use constant DEBUG => 0; line and changing it to 1) in Chado.pm and trying to load a region.  That will produce an enormous amount of output in the apache error_log, and you can send that as an attachment to the list if nothing obvious jumps out at you.
 

Scott




On Thu, Oct 16, 2014 at 5:21 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi there,
 
 
 I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems now.http://www.pichiagenome.org/ is the site
 
 
 1) Most of the time there is an error message popping up I can't figure out the reason for:
 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK: Bio::Graphics::Browser2::Region::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK: Bio::Graphics::Browser2::Region::lookup_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK: Bio::Graphics::Browser2::Region::search_db /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK: /usr/lib/cgi-bin/gb2/gbrowse:50
 
 
 2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore
 
 
 This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.
 
 
 I would appreciate any hint for solving this problems
 
 
 
 
 
 Thank you
 
 
 Nadine
 
 
 
 
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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
 


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Re: 2 Problems concerning track loading/Error Message

Nadine Elpida Tatto
In reply to this post by Scott Cain
Hi Scott,

Following the error.log content from setting DEBUG=1:

[...]
Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] in get_feature_by_name, args:-name FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1332., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] name:FR839628 in get_feature_by_name at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1391., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] first get_feature_by_name query:select f.feature_id  FROM  feature f where f.searchable_name @@ to_tsquery(?)  AND f.organism_id =13 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1513., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:2366 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:accession:GenBank, dbxref_id:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6770 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6937 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:3 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] FR839628 might be a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1578., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] Yep, FR839628 is a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1591., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] srcfeature args:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1597., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3287e50), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x27c1458), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3151a68), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x1e44340), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[...]

Is this helpful?

Nadine


>>> Scott Cain <[hidden email]> 10/16/14 2:38 PM >>>
Hi Nadine,
That error message isn't much to go on; that message comes from the work-horse method that does name searching in the Chado adaptor, so quite a few things could be going on.

Just to be clear--the site worked fine a few weeks ago but now does not, right?  So the question is, what changed?  Did GBrowse, BioPerl or Postgres get updated?  Was data added or deleted from the Chado database?  Was full text searching turned on with out prepping the database?

If none of these things appear to be the case, I'd suggest turning on DEBUG (locating the use constant DEBUG => 0; line and changing it to 1) in Chado.pm and trying to load a region.  That will produce an enormous amount of output in the apache error_log, and you can send that as an attachment to the list if nothing obvious jumps out at you.

Scott


On Thu, Oct 16, 2014 at 5:21 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi there,


I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems now.http://www.pichiagenome.org/ is the site


1) Most of the time there is an error message popping up I can't figure out the reason for:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK: Bio::Graphics::Browser2::Region::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK: Bio::Graphics::Browser2::Region::lookup_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK: Bio::Graphics::Browser2::Region::search_db /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK: /usr/lib/cgi-bin/gb2/gbrowse:50


2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore


This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.


I would appreciate any hint for solving this problems





Thank you


Nadine




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Re: 2 Problems concerning track loading/Error Message

Scott Cain
Hi Nadine,

The Chado adaptor has been configured to use full text searching, which I can tell because it is building queries that use those functions (the "@@" in the query gives that away), but I don't think the tools to create the full text indexes have been created, which is why it gives messages about the text-search query containing stop words or nothing.

There are two potential fixes, either remove the full text searching directive from the config, or build the index.  See http://gmod.org/wiki/Chado_Full_Text_Search for more information.

Scott


On Thu, Oct 16, 2014 at 9:56 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi Scott,

Following the error.log content from setting DEBUG=1:

[...]
Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] in get_feature_by_name, args:-name FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1332., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] name:FR839628 in get_feature_by_name at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1391., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] first get_feature_by_name query:select f.feature_id  FROM  feature f where f.searchable_name @@ to_tsquery(?)  AND f.organism_id =13 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1513., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:2366 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:accession:GenBank, dbxref_id:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6770 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6937 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:3 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] FR839628 might be a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1578., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] Yep, FR839628 is a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1591., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] srcfeature args:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1597., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3287e50), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x27c1458), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3151a68), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x1e44340), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[...]

Is this helpful?

Nadine


>>> Scott Cain <[hidden email]> 10/16/14 2:38 PM >>>
Hi Nadine,
That error message isn't much to go on; that message comes from the work-horse method that does name searching in the Chado adaptor, so quite a few things could be going on.

Just to be clear--the site worked fine a few weeks ago but now does not, right?  So the question is, what changed?  Did GBrowse, BioPerl or Postgres get updated?  Was data added or deleted from the Chado database?  Was full text searching turned on with out prepping the database?

If none of these things appear to be the case, I'd suggest turning on DEBUG (locating the use constant DEBUG => 0; line and changing it to 1) in Chado.pm and trying to load a region.  That will produce an enormous amount of output in the apache error_log, and you can send that as an attachment to the list if nothing obvious jumps out at you.

Scott


On Thu, Oct 16, 2014 at 5:21 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi there,


I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems now.http://www.pichiagenome.org/ is the site


1) Most of the time there is an error message popping up I can't figure out the reason for:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK: Bio::Graphics::Browser2::Region::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK: Bio::Graphics::Browser2::Region::lookup_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK: Bio::Graphics::Browser2::Region::search_db /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK: /usr/lib/cgi-bin/gb2/gbrowse:50


2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore


This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.


I would appreciate any hint for solving this problems





Thank you


Nadine




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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

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Re: 2 Problems concerning track loading/Error Message

Nadine Elpida Tatto
Thank you :-)

I will try to fix it with your infos.

Nadine

>>> Scott Cain <[hidden email]> 10/16/14 4:04 PM >>>
Hi Nadine,
The Chado adaptor has been configured to use full text searching, which I can tell because it is building queries that use those functions (the "@@" in the query gives that away), but I don't think the tools to create the full text indexes have been created, which is why it gives messages about the text-search query containing stop words or nothing.

There are two potential fixes, either remove the full text searching directive from the config, or build the index.  See http://gmod.org/wiki/Chado_Full_Text_Search for more information.

Scott


On Thu, Oct 16, 2014 at 9:56 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi Scott,

Following the error.log content from setting DEBUG=1:

[...]
Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] in get_feature_by_name, args:-name FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1332., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] name:FR839628 in get_feature_by_name at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1391., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] first get_feature_by_name query:select f.feature_id  FROM  feature f where f.searchable_name @@ to_tsquery(?)  AND f.organism_id =13 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1513., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:2366 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:accession:GenBank, dbxref_id:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6770 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6937 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:3 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] FR839628 might be a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1578., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] Yep, FR839628 is a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1591., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] srcfeature args:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1597., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3287e50), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x27c1458), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3151a68), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x1e44340), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[...]

Is this helpful?

Nadine


>>> Scott Cain <[hidden email]> 10/16/14 2:38 PM >>>
Hi Nadine,
That error message isn't much to go on; that message comes from the work-horse method that does name searching in the Chado adaptor, so quite a few things could be going on.

Just to be clear--the site worked fine a few weeks ago but now does not, right?  So the question is, what changed?  Did GBrowse, BioPerl or Postgres get updated?  Was data added or deleted from the Chado database?  Was full text searching turned on with out prepping the database?

If none of these things appear to be the case, I'd suggest turning on DEBUG (locating the use constant DEBUG => 0; line and changing it to 1) in Chado.pm and trying to load a region.  That will produce an enormous amount of output in the apache error_log, and you can send that as an attachment to the list if nothing obvious jumps out at you.

Scott


On Thu, Oct 16, 2014 at 5:21 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi there,


I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems now.http://www.pichiagenome.org/ is the site


1) Most of the time there is an error message popping up I can't figure out the reason for:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK: Bio::Graphics::Browser2::Region::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK: Bio::Graphics::Browser2::Region::lookup_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK: Bio::Graphics::Browser2::Region::search_db /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK: /usr/lib/cgi-bin/gb2/gbrowse:50


2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore


This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.


I would appreciate any hint for solving this problems





Thank you


Nadine




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Scott Cain, Ph. D.                                   scott at scottcain dot net
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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

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Re: 2 Problems concerning track loading/Error Message

Nadine Elpida Tatto
In reply to this post by Scott Cain
Hi Scott,

it seems that this fixed the big red error message (I changed the flag in the conf-file to 0), but unfortunately not the issue with the non displaying features. Do you have any suggestions how I could fix that?

There is still this error in the apache log:

[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275

This is how the conf files according the db look like now:
[scaffolds:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn dbi:Pg:dbname=chado_pipa_GS115;host=localhost;port=xxxx
                -user xxx
                -pass xxx
                -organism "pichia pastoris"
                -srcfeatureslice 1
                -fulltext 0
search options = all +autocomplete

Thanks a lot in advance

Nadine



>>> Scott Cain <[hidden email]> 10/16/14 4:04 PM >>>
Hi Nadine,
The Chado adaptor has been configured to use full text searching, which I can tell because it is building queries that use those functions (the "@@" in the query gives that away), but I don't think the tools to create the full text indexes have been created, which is why it gives messages about the text-search query containing stop words or nothing.

There are two potential fixes, either remove the full text searching directive from the config, or build the index.  See http://gmod.org/wiki/Chado_Full_Text_Search for more information.

Scott


On Thu, Oct 16, 2014 at 9:56 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi Scott,

Following the error.log content from setting DEBUG=1:

[...]
Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] in get_feature_by_name, args:-name FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1332., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] name:FR839628 in get_feature_by_name at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1391., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] first get_feature_by_name query:select f.feature_id  FROM  feature f where f.searchable_name @@ to_tsquery(?)  AND f.organism_id =13 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1513., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:2366 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:accession:GenBank, dbxref_id:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6770 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6937 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:3 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] FR839628 might be a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1578., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] Yep, FR839628 is a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1591., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] srcfeature args:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1597., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3287e50), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x27c1458), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3151a68), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x1e44340), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[...]

Is this helpful?

Nadine


>>> Scott Cain <[hidden email]> 10/16/14 2:38 PM >>>
Hi Nadine,
That error message isn't much to go on; that message comes from the work-horse method that does name searching in the Chado adaptor, so quite a few things could be going on.

Just to be clear--the site worked fine a few weeks ago but now does not, right?  So the question is, what changed?  Did GBrowse, BioPerl or Postgres get updated?  Was data added or deleted from the Chado database?  Was full text searching turned on with out prepping the database?

If none of these things appear to be the case, I'd suggest turning on DEBUG (locating the use constant DEBUG => 0; line and changing it to 1) in Chado.pm and trying to load a region.  That will produce an enormous amount of output in the apache error_log, and you can send that as an attachment to the list if nothing obvious jumps out at you.

Scott


On Thu, Oct 16, 2014 at 5:21 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi there,


I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems now.http://www.pichiagenome.org/ is the site


1) Most of the time there is an error message popping up I can't figure out the reason for:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK: Bio::Graphics::Browser2::Region::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK: Bio::Graphics::Browser2::Region::lookup_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK: Bio::Graphics::Browser2::Region::search_db /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK: /usr/lib/cgi-bin/gb2/gbrowse:50


2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore


This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.


I would appreciate any hint for solving this problems





Thank you


Nadine




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GMOD Coordinator (http://gmod.org/)                     216-392-3087
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Re: 2 Problems concerning track loading/Error Message

Scott Cain
Hi Nadine,

While this is not likely the problem, double check that the name of the organism (including case) is spelled correctly:

  SELECT * FROM organism WHERE name='pichia pastoris';

The only reason it occurs to me to ask is that it is typical to capitalize the P in Pichia.

Scott

On Thu, Oct 16, 2014 at 11:18 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi Scott,

it seems that this fixed the big red error message (I changed the flag in the conf-file to 0), but unfortunately not the issue with the non displaying features. Do you have any suggestions how I could fix that?

There is still this error in the apache log:

[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275

This is how the conf files according the db look like now:
[scaffolds:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn dbi:Pg:dbname=chado_pipa_GS115;host=localhost;port=xxxx
                -user xxx
                -pass xxx
                -organism "pichia pastoris"
                -srcfeatureslice 1
                -fulltext 0
search options = all +autocomplete

Thanks a lot in advance

Nadine



>>> Scott Cain <[hidden email]> 10/16/14 4:04 PM >>>

Hi Nadine,
The Chado adaptor has been configured to use full text searching, which I can tell because it is building queries that use those functions (the "@@" in the query gives that away), but I don't think the tools to create the full text indexes have been created, which is why it gives messages about the text-search query containing stop words or nothing.

There are two potential fixes, either remove the full text searching directive from the config, or build the index.  See http://gmod.org/wiki/Chado_Full_Text_Search for more information.

Scott


On Thu, Oct 16, 2014 at 9:56 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi Scott,

Following the error.log content from setting DEBUG=1:

[...]
Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] in get_feature_by_name, args:-name FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1332., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] name:FR839628 in get_feature_by_name at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1391., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] first get_feature_by_name query:select f.feature_id  FROM  feature f where f.searchable_name @@ to_tsquery(?)  AND f.organism_id =13 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1513., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:2366 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:accession:GenBank, dbxref_id:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6770 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6937 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:3 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] FR839628 might be a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1578., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] Yep, FR839628 is a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1591., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] srcfeature args:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1597., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3287e50), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x27c1458), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3151a68), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x1e44340), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[...]

Is this helpful?

Nadine


>>> Scott Cain <[hidden email]> 10/16/14 2:38 PM >>>
Hi Nadine,
That error message isn't much to go on; that message comes from the work-horse method that does name searching in the Chado adaptor, so quite a few things could be going on.

Just to be clear--the site worked fine a few weeks ago but now does not, right?  So the question is, what changed?  Did GBrowse, BioPerl or Postgres get updated?  Was data added or deleted from the Chado database?  Was full text searching turned on with out prepping the database?

If none of these things appear to be the case, I'd suggest turning on DEBUG (locating the use constant DEBUG => 0; line and changing it to 1) in Chado.pm and trying to load a region.  That will produce an enormous amount of output in the apache error_log, and you can send that as an attachment to the list if nothing obvious jumps out at you.

Scott


On Thu, Oct 16, 2014 at 5:21 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi there,


I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems now.http://www.pichiagenome.org/ is the site


1) Most of the time there is an error message popping up I can't figure out the reason for:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK: Bio::Graphics::Browser2::Region::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK: Bio::Graphics::Browser2::Region::lookup_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK: Bio::Graphics::Browser2::Region::search_db /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK: /usr/lib/cgi-bin/gb2/gbrowse:50


2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore


This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.


I would appreciate any hint for solving this problems





Thank you


Nadine




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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
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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

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Re: 2 Problems concerning track loading/Error Message

Scott Cain
Also, other things you might want to try: 

* deleting all of the cookies associated with this server.

* removing the "autocomplete" because the Chado adaptor doesn't support it (but it shouldn't make a difference).

If none of these things do it, I'll see if I can write a command line script that might test and help us figure out the problem.

On Thu, Oct 16, 2014 at 11:23 AM, Scott Cain <[hidden email]> wrote:
Hi Nadine,

While this is not likely the problem, double check that the name of the organism (including case) is spelled correctly:

  SELECT * FROM organism WHERE name='pichia pastoris';

The only reason it occurs to me to ask is that it is typical to capitalize the P in Pichia.

Scott

On Thu, Oct 16, 2014 at 11:18 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi Scott,

it seems that this fixed the big red error message (I changed the flag in the conf-file to 0), but unfortunately not the issue with the non displaying features. Do you have any suggestions how I could fix that?

There is still this error in the apache log:

[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275

This is how the conf files according the db look like now:
[scaffolds:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn dbi:Pg:dbname=chado_pipa_GS115;host=localhost;port=xxxx
                -user xxx
                -pass xxx
                -organism "pichia pastoris"
                -srcfeatureslice 1
                -fulltext 0
search options = all +autocomplete

Thanks a lot in advance

Nadine



>>> Scott Cain <[hidden email]> 10/16/14 4:04 PM >>>

Hi Nadine,
The Chado adaptor has been configured to use full text searching, which I can tell because it is building queries that use those functions (the "@@" in the query gives that away), but I don't think the tools to create the full text indexes have been created, which is why it gives messages about the text-search query containing stop words or nothing.

There are two potential fixes, either remove the full text searching directive from the config, or build the index.  See http://gmod.org/wiki/Chado_Full_Text_Search for more information.

Scott


On Thu, Oct 16, 2014 at 9:56 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi Scott,

Following the error.log content from setting DEBUG=1:

[...]
Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] in get_feature_by_name, args:-name FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1332., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] name:FR839628 in get_feature_by_name at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1391., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] first get_feature_by_name query:select f.feature_id  FROM  feature f where f.searchable_name @@ to_tsquery(?)  AND f.organism_id =13 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1513., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:2366 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:accession:GenBank, dbxref_id:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6770 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6937 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:3 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] FR839628 might be a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1578., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] Yep, FR839628 is a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1591., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] srcfeature args:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1597., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3287e50), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x27c1458), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3151a68), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x1e44340), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[...]

Is this helpful?

Nadine


>>> Scott Cain <[hidden email]> 10/16/14 2:38 PM >>>
Hi Nadine,
That error message isn't much to go on; that message comes from the work-horse method that does name searching in the Chado adaptor, so quite a few things could be going on.

Just to be clear--the site worked fine a few weeks ago but now does not, right?  So the question is, what changed?  Did GBrowse, BioPerl or Postgres get updated?  Was data added or deleted from the Chado database?  Was full text searching turned on with out prepping the database?

If none of these things appear to be the case, I'd suggest turning on DEBUG (locating the use constant DEBUG => 0; line and changing it to 1) in Chado.pm and trying to load a region.  That will produce an enormous amount of output in the apache error_log, and you can send that as an attachment to the list if nothing obvious jumps out at you.

Scott


On Thu, Oct 16, 2014 at 5:21 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi there,


I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems now.http://www.pichiagenome.org/ is the site


1) Most of the time there is an error message popping up I can't figure out the reason for:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK: Bio::Graphics::Browser2::Region::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK: Bio::Graphics::Browser2::Region::lookup_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK: Bio::Graphics::Browser2::Region::search_db /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK: /usr/lib/cgi-bin/gb2/gbrowse:50


2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore


This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.


I would appreciate any hint for solving this problems





Thank you


Nadine




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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
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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

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Re: 2 Problems concerning track loading/Error Message

Nadine Elpida Tatto
Dear Scott,


In the meantime I've tried out, what you wrote me:


1) The is no column 'name' - only common_name in my organism table. An in this column P.pastoris is not written with a capital letter.


chado_pipa_DSMZ=> SELECT * FROM organism WHERE name='pichia pastoris';
ERROR:  column "name" does not exist
LINE 1: SELECT * FROM organism WHERE name='pichia pastoris';
                                     ^
chado_pipa_DSMZ=> select * from organism
chado_pipa_DSMZ-> ;
 organism_id |  abbreviation  |     genus      |   species    |   common_name   | comment 
-------------+----------------+----------------+--------------+-----------------+---------
           1 | H.sapiens      | Homo           | sapiens      | human           | 
           2 | D.melanogaster | Drosophila     | melanogaster | fruitfly        | 
           3 | M.musculus     | Mus            | musculus     | mouse           | 
           4 | A.gambiae      | Anopheles      | gambiae      | mosquito        | 
           5 | R.norvegicus   | Rattus         | norvegicus   | rat             | 
           6 | A.thaliana     | Arabidopsis    | thaliana     | mouse-ear cress | 
           7 | C.elegans      | Caenorhabditis | elegans      | worm            | 
           8 | D.rerio        | Danio          | rerio        | zebrafish       | 
           9 | O.sativa       | Oryza          | sativa       | rice            | 
          10 | S.cerevisiae   | Saccharomyces  | cerevisiae   | yeast           | 
          11 | X.laevis       | Xenopus        | laevis       | frog            | 
          12 | D.discoideum   | Dictyostelium  | discoideum   | dicty           | 
          13 | P.pastoris     | Pichia         | pastoris     | pichia pastoris | 
(13 rows)


2) I've cleared all browser cookies and the browser cach and I've cleared all tmp files on the serversite I could find (/var/tmp and /var/www/tmp/images/)
3) autocomplete was removed from the conf-files


Unfortunately nothing of these helped and there is still nothing displayed....


If you have any further idea how I could determin the source of this problem I would be really happy.


Nadine







>>> Scott Cain <[hidden email]> 10/16/14 5:29 PM >>>
Also, other things you might want to try: 

* deleting all of the cookies associated with this server.


* removing the "autocomplete" because the Chado adaptor doesn't support it (but it shouldn't make a difference).


If none of these things do it, I'll see if I can write a command line script that might test and help us figure out the problem.


On Thu, Oct 16, 2014 at 11:23 AM, Scott Cain <[hidden email]> wrote:
Hi Nadine,

While this is not likely the problem, double check that the name of the organism (including case) is spelled correctly:


  SELECT * FROM organism WHERE name='pichia pastoris';


The only reason it occurs to me to ask is that it is typical to capitalize the P in Pichia.


Scott


On Thu, Oct 16, 2014 at 11:18 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi Scott,


it seems that this fixed the big red error message (I changed the flag in the conf-file to 0), but unfortunately not the issue with the non displaying features. Do you have any suggestions how I could fix that?


There is still this error in the apache log:


[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275
[Thu Oct 16 16:24:34 2014] [error] [client 141.244.140.143] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=contig00275


This is how the conf files according the db look like now:
[scaffolds:database]
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn dbi:Pg:dbname=chado_pipa_GS115;host=localhost;port=xxxx
                -user xxx
                -pass xxx
                -organism "pichia pastoris"
                -srcfeatureslice 1
                -fulltext 0
search options = all +autocomplete


Thanks a lot in advance

Nadine





>>> Scott Cain <[hidden email]> 10/16/14 4:04 PM >>>
Hi Nadine,
The Chado adaptor has been configured to use full text searching, which I can tell because it is building queries that use those functions (the "@@" in the query gives that away), but I don't think the tools to create the full text indexes have been created, which is why it gives messages about the text-search query containing stop words or nothing.

There are two potential fixes, either remove the full text searching directive from the config, or build the index.  See http://gmod.org/wiki/Chado_Full_Text_Search for more information.

Scott



On Thu, Oct 16, 2014 at 9:56 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi Scott,

Following the error.log content from setting DEBUG=1:

[...]
Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] in get_feature_by_name, args:-name FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1332., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] name:FR839628 in get_feature_by_name at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1391., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] first get_feature_by_name query:select f.feature_id  FROM  feature f where f.searchable_name @@ to_tsquery(?)  AND f.organism_id =13 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1513., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:2366 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:accession:GenBank, dbxref_id:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6770 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:6937 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] src_name:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1634., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] d2s:dbxref:92320, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] feature_id in features method loop:3 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1571., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] FR839628 might be a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1578., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] Yep, FR839628 is a srcfeature at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1591., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 2014] [error] [client xxx.xxx.xxx.xxx] srcfeature args:FR839628 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1597., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:21 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaDSMZ/?name=id:333;dbid=scaffolds:database
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3287e50), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:22 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x27c1458), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:32 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 www-data .config/inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Reverting coordinates to last known good region (user probably hit 'back' button). at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2818., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x3151a68), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value $name in pattern match (m//) at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm line 464., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm line 2874., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Can't call method "seq_id" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RenderPanels.pm line 2046., referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:41:33 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: gbrowse, referer: http://gbrowse.dswm.at/cgi-bin/gb2/gbrowse/pipaCBS7435/?name=FR839631%3A1350000..1670000
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] DBI::db=HASH(0x1e44340), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] SOFA id to use: 18 at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 254., referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] cvterm query: select ct.cvterm_id,ct.name as name, c.name as cvname, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            from cvterm ct, cv c, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            where ct.cv_id=c.cv_id and, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                            (c.name IN (, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'relationship type','Relationship Ontology',, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                                'autocreated'), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx]                             OR c.cv_id = ?), referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/
[Thu Oct 16 15:45:46 2014] [error] [client xxx.xxx.xxx.xxx] NOTICE:  text-search query contains only stop words or doesn't contain lexemes, ignored, referer: http://www.pichiagenome.org/

[...]

Is this helpful?

Nadine


>>> Scott Cain <[hidden email]> 10/16/14 2:38 PM >>>
Hi Nadine,
That error message isn't much to go on; that message comes from the work-horse method that does name searching in the Chado adaptor, so quite a few things could be going on.

Just to be clear--the site worked fine a few weeks ago but now does not, right?  So the question is, what changed?  Did GBrowse, BioPerl or Postgres get updated?  Was data added or deleted from the Chado database?  Was full text searching turned on with out prepping the database?

If none of these things appear to be the case, I'd suggest turning on DEBUG (locating the use constant DEBUG => 0; line and changing it to 1) in Chado.pm and trying to load a region.  That will produce an enormous amount of output in the apache error_log, and you can send that as an attachment to the list if nothing obvious jumps out at you.
 
Scott



On Thu, Oct 16, 2014 at 5:21 AM, Nadine Elpida Tatto <[hidden email]> wrote:
Hi there,
 
 
 I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems now.http://www.pichiagenome.org/ is the site
 
 
 1) Most of the time there is an error message popping up I can't figure out the reason for:
 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK: Bio::Graphics::Browser2::Region::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK: Bio::Graphics::Browser2::Region::lookup_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK: Bio::Graphics::Browser2::Region::search_db /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK: Bio::Graphics::Browser2::RegionSearch::search_features_locally /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK: Bio::Graphics::Browser2::RegionSearch::search_features /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK: Bio::Graphics::Browser2::Render::region /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK: Bio::Graphics::Browser2::Render::segment /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK: Bio::Graphics::Browser2::Render::_update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK: Bio::Graphics::Browser2::Render::update_state /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK: Bio::Graphics::Browser2::Render::run /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK: /usr/lib/cgi-bin/gb2/gbrowse:50
 
 
 2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore
 
 
 This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.
 
 
 I would appreciate any hint for solving this problems
 
 
 
 
 
 Thank you
 
 
 Nadine
 
 
 
 
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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 
 



 



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research 
 



 




-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research 
 






-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research 
 


------------------------------------------------------------------------------
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://p.sf.net/sfu/Zoho
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse