[Bioperl-l] New GO Parser and errors loading biosql database
Law, Annie
Annie.Law at nrc-cnrc.gc.ca
Thu Feb 19 15:50:10 EST 2004
Hi Hilmar,
Thanks for the tips. I got the GO to go. I have some questions about the GO
loading result, bioperl-db make test and overall
Order of loading a database.
1) I installed the Graph module and loading of the GO information into an
empty databse seems to
run okay in the safe mode. However, many of the entries are not able to be
inserted (roughly 200).
Mostly complaining about how the column name cannot be null. However, I'm
not sure if it is related to
The make test errors I am having with bioperl-db that I have listed below or
if this is an acceptable result.
In general how should a user gauge how successful a load of the database
was? I guess you can sort
of look at the total number of expected number entries.
-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values were
("BBD_pathwayID:C1cyc","","","") FKs (2)
Column 'name' cannot be null
---------------------------------------------------
Could not store BBD_pathwayID:C1cyc ():
------------- EXCEPTION -------------
MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be found
by unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253
STACK Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:270
STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
--------------------------------------
-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values were
("BBD_pathwayID:abs","","","") FKs (3)
Column 'name' cannot be null
---------------------------------------------------
Could not store BBD_pathwayID:abs ():
------------- EXCEPTION -------------
MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be found
by unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253
STACK Bio::DB::Persistent::PersistentObject::store
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:270
STACK (eval) /root/bioperl-db/scripts/biosql/load_ontology.pl:508
STACK toplevel /root/bioperl-db/scripts/biosql/load_ontology.pl:490
--------------------------------------
2) I have a question about The make test bioperl-db results which may be
related to the results that I am getting. I seem to be having problems with
the make test for bioperl-db. I downloaded the tarball from the CVS website
and installed it.
I looked at the documentation and I created User biosql which has been given
all the permissions it needs. I also renamed the files as stated in the
steps below. In the t directory of bioperl-db $ cd t $ cp
DBHarness.conf.example DBHarness.biosql.conf $ cp DBHarness.conf.example
DBHarness.markerdb.conf
I also put a copy of those file in the bioperl-db in the home directory
since that was documented for the newest version
Of bioperl-db.
I did a make test in the bioperl-db directory and go the following results.
Most of the tests seem to fail. I am not sure why.
[root at microarray bioperl-db]# maket test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/cluster.......install_driver(mysql) failed: Can't load
'/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mys
ql.so' for module DBD::mysql:
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mysq
l.so: undefined symbol: mysql_ssl_set at
/usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229. at
(eval 4) line 3 Compilation failed in require at (eval 4) line 3. Perhaps a
required shared library or dll isn't installed where expected at
t/DBTestHarness.pm line 211
t/cluster.......dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-160
Failed 160/160 tests, 0.00% okay
t/comment.......install_driver(mysql) failed: Can't load
'/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mys
ql.so' for module DBD::mysql:
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mysq
l.so: undefined symbol: mysql_ssl_set at
/usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229. at
(eval 4) line 3 Compilation failed in require at (eval 4) line 3. Perhaps a
required shared library or dll isn't installed where expected at
t/DBTestHarness.pm line 211
t/comment.......dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-11
Failed 11/11 tests, 0.00% okay
t/dbadaptor.....install_driver(mysql) failed: Can't load
'/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mys
ql.so' for module DBD::mysql:
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mysq
l.so: undefined symbol: mysql_ssl_set at
/usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229. at
(eval 5) line 3 Compilation failed in require at (eval 5) line 3. Perhaps a
required shared library or dll isn't installed where expected at
t/DBTestHarness.pm line 211
t/swiss.........dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-52
Failed 52/52 tests, 0.00% okay
Failed Test Stat Wstat Total Fail Failed List of Failed
----------------------------------------------------------------------------
---
t/cluster.t 255 65280 160 160 100.00% 1-160
t/comment.t 255 65280 11 11 100.00% 1-11
t/dbadaptor.t 255 65280 6 6 100.00% 1-6
t/dblink.t 255 65280 18 18 100.00% 1-18
t/ensembl.t 255 65280 15 15 100.00% 1-15
t/fuzzy2.t 255 65280 21 21 100.00% 1-21
t/genbank.t 255 65280 18 18 100.00% 1-18
t/locuslink.t 255 65280 110 110 100.00% 1-110
t/ontology.t 255 65280 302 302 100.00% 1-302
t/remove.t 255 65280 59 59 100.00% 1-59
t/seqfeature.t 255 65280 48 48 100.00% 1-48
t/simpleseq.t 255 65280 27 27 100.00% 1-27
t/species.t 255 65280 65 65 100.00% 1-65
t/swiss.t 255 65280 52 52 100.00% 1-52
Failed 14/15 test scripts, 6.67% okay. 912/930 subtests failed, 1.94% okay.
make: *** [test_dynamic] Error 2
3) Previously when I did a make test for the Bioperl 1.4 installation most
of the tests passed 97% I'm not sure whether the errors are expected or not
Here are the results of the make test. I only cut out the beginning of the
test and the summary at the end. Installation of bioperl
------------- EXCEPTION -------------
MSG: Failed to load module Bio::SeqIO::game. Can't locate IO/String.pm in
@INC (@INC contains: . t /root/bioperl-1.4/blib/lib
/root/bioperl-1.4/blib/arch /usr/lib/perl5/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl) at
Bio/SeqIO/game/gameWriter.pm line 63. BEGIN failed--compilation aborted at
Bio/SeqIO/game/gameWriter.pm line 63. Compilation failed in require at
Bio/SeqIO/game.pm line 77. BEGIN failed--compilation aborted at
Bio/SeqIO/game.pm line 77. Compilation failed in require at
/root/bioperl-1.4/blib/lib/Bio/Root/Root.pm line 394.
STACK Bio::Root::Root::_load_module
/root/bioperl-1.4/blib/lib/Bio/Root/Root.pm:396
STACK (eval) /root/bioperl-1.4/blib/lib/Bio/SeqIO.pm:549
STACK Bio::SeqIO::_load_format_module
/root/bioperl-1.4/blib/lib/Bio/SeqIO.pm:548
STACK Bio::SeqIO::new /root/bioperl-1.4/blib/lib/Bio/SeqIO.pm:377
STACK (eval) /root/bioperl-1.4/blib/lib/bptutorial.pl:4027
STACK main::__ANON__ /root/bioperl-1.4/blib/lib/bptutorial.pl:4025
STACK main::run_examples /root/bioperl-1.4/blib/lib/bptutorial.pl:4152
STACK toplevel t/tutorial.t:23
--------------------------------------
For more information about the SeqIO system please see the SeqIO docs. This
includes ways of checking for formats at compile time, not run time Can't
call method "next_seq" on an undefined value at
/root/bioperl-1.4/blib/lib/bptutorial.pl line 4035.
Failed Test Stat Wstat Total Fail Failed List of Failed
----------------------------------------------------------------------------
---
t/BioDBGFF.t 133 133 100.00% 1-133
t/ESEfinder.t 2 512 12 0 0.00% ??
t/GuessSeqFormat.t 2 512 46 46 100.00% 1-46
t/SeqFeature.t 25 6400 74 0 0.00% ??
t/tutorial.t 2 512 21 3 14.29% 19-21
22 subtests skipped.
Failed 5/179 test scripts, 97.21% okay. 182/8122 subtests failed, 97.76%
okay.
make: *** [test_dynamic] Error 29
#end of installation of bioperl
4) Also, hopefully when I get this all running I would like to know what is
the best order for loading the database. I know you mentionned that the GO
database information should be loaded before the locuslink information. Here
is the list of proposed order of entering information into the database.
Can you use load_seqdatabase.pl for loading unigene information?
1. load NCBI taxonomy database with load_ncbi_taxonomy.pl
2. GO information
3. load locuslink database information
4. unigene information which I also had problems with loading information
in
[root@ bioperl-1.4]#perl /root/bioperl-db/scripts/biosql/load_seqdatabase.pl
--dbuser=root --dbpass=ms22 --dbname bioseqdb
--namespace "Unigene" -format unigene /root/bioperl--1.4/unigenedata/Hs.data
Loading /root/bioperl-1.4/unigenedata/Hs.data ...
Bio::SeqIO: unigene cannot be found
Exception
------------- EXCEPTION -------------
MSG: Failed to load module Bio::SeqIO::unigene. Can't locate
Bio/SeqIO/unigene.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 394.
STACK Bio::Root::Root::_load_module
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm:396
STACK (eval) /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO.pm:549
STACK Bio::SeqIO::_load_format_module
/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO.pm:548
STACK Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO.pm:377
STACK toplevel /root/bioperl-db/scripts/biosql/load_seqdatabase.pl:436
--------------------------------------
For more information about the SeqIO system please see the SeqIO docs. This
includes ways of checking for formats at compile time, not run time Can't
call method "next_seq" on an undefined value at
/root/bioperl-db/scripts/biosql/load_seqdatabase.pl line 460.
Thanks very much,
Annie.
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