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
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 <***@scottcain.net> 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 <***@boku.ac.at> 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
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 <***@boku.ac.at> 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
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 <***@boku.ac.at> 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