[GUSDEV] InsertGOTermsFromObo

[davila <da...@io...>]

Dear All,

I just downloaded and installed ApiCommonData plugins to our GUS 3.5 =
Postgres install , then ran:

nohup ga ApiCommonData::Load::Plugin::InsertGOTermsFromObo --oboFile
/home/user/GO/gene_ontology_edit.obo.2007-07-01 --extDbRlsName "Gene
Ontology" --extDbRlsVer 5.375 --commit >
/home/user/log/ga_ApiCommonData_InsertGOTermsFromObo_GeneOntology.log &

It loaded many GO terms into the SRes.GOTerms table (not sure if all of =
them) but also generated a huge log file (bigger than 25GB) with the =
errors listed below... any ideas on how to solve this ? Thanks, Alberto.

[user@server log]$ more
ga_ApiCommonData_InsertGOTermsFromObo_GeneOntology.log
Wed Jul 25 13:06:50 2007        DSN     dbi:Pg:dbname=3Dmydb
Wed Jul 25 13:06:50 2007        PLUGIN
ApiCommonData::Load::Plugin::InsertGOTermsFromObo
Wed Jul 25 13:06:50 2007        ARG     algoinvo        1
Wed Jul 25 13:06:50 2007        ARG     comment
Wed Jul 25 13:06:50 2007        ARG     commit  1
Wed Jul 25 13:06:50 2007        ARG     debug   0
Wed Jul 25 13:06:50 2007        ARG     extDbRlsName    Gene Ontology
Wed Jul 25 13:06:50 2007        ARG     extDbRlsVer     5.375
Wed Jul 25 13:06:50 2007        ARG     group
Wed Jul 25 13:06:50 2007        ARG     gusconfigfile
$GUS_HOME/config/gus.config
Wed Jul 25 13:06:50 2007        ARG     help
Wed Jul 25 13:06:50 2007        ARG     helpHTML
Wed Jul 25 13:06:50 2007        ARG     oboFile
/home/user/GO/gene_ontology_edit.obo.2007-07-01
Wed Jul 25 13:06:50 2007        ARG     project
Wed Jul 25 13:06:50 2007        ARG     sqlVerbose      0
Wed Jul 25 13:06:50 2007        ARG     user
Wed Jul 25 13:06:50 2007        ARG     verbose 0
Wed Jul 25 13:06:50 2007        ARG     veryVerbose     0
Wed Jul 25 13:06:50 2007        AlgInvocationId 461
Wed Jul 25 13:06:50 2007        COMMIT  commit on
Processed 500 terms
Processed 1000 terms
Processed 1500 terms
Processed 2000 terms
Processed 2500 terms
Processed 3000 terms
Processed 3500 terms
Processed 4000 terms
Processed 4500 terms
Processed 5000 terms
Processed 5500 terms
Processed 6000 terms
Processed 6500 terms
Processed 7000 terms
Processed 7500 terms
Processed 8000 terms
Processed 8500 terms
Processed 9000 terms
Processed 9500 terms
Processed 10000 terms
Processed 10500 terms
Processed 11000 terms
Processed 11500 terms
Processed 12000 terms
Processed 12500 terms
Processed 13000 terms
Processed 13500 terms
Processed 14000 terms
Processed 14500 terms
Processed 15000 terms
Processed 15500 terms
Processed 16000 terms
Processed 16500 terms
Processed 17000 terms
Processed 17500 terms
Processed 18000 terms
Processed 18500 terms
Processed 19000 terms
Processed 19500 terms
Processed 20000 terms
Processed 20500 terms
Processed 21000 terms
Processed 21500 terms
Processed 22000 terms
Processed 22500 terms
Processed 23000 terms
Processed 23500 terms
Processed 24000 terms
DBD::Pg::db do failed: ERROR:  table "go_tc" does not exist
DBD::Pg::db do failed: ERROR:  syntax error at or near "(" at character =
47
DBD::Pg::db do failed: ERROR:  current transaction is aborted, commands
ignored until end of transaction block
DBD::Pg::db do failed: ERROR:  current transaction is aborted, commands
ignored until end of transaction block
DBD::Pg::db selectrow_array failed: ERROR:  current transaction is
aborted, commands ignored until end of transaction block
DBD::Pg::db selectrow_array failed: ERROR:  current transaction is
aborted, commands ignored until end of transaction block
GO Terms:
DBD::Pg::db selectrow_array failed: ERROR:  current transaction is
aborted, commands ignored until end of transaction block
Relationships:
starting size:
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block
DBD::Pg::st fetchrow_array failed: no statement executing
Transitive closure (length 2): added 0 edges
DBD::Pg::st execute failed: ERROR:  prepared statement "dbdpg_2" does
not exist
DBD::Pg::st fetchrow_array failed: no statement executing
Transitive closure (length 3): added 0 edges
DBD::Pg::st execute failed: ERROR:  prepared statement "dbdpg_2" does
not exist
DBD::Pg::st fetchrow_array failed: no statement executing
Transitive closure (length 4): added 0 edges
DBD::Pg::st execute failed: ERROR:  prepared statement "dbdpg_2" does
not exist=20