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[Gusdev-gusdev] LoadPfam plugin error:
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From: MICHAEL L. <lu...@cs...> - 2003-05-28 20:56:18
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Hello all
While attempting to use the LoadPfam plugin I have gotten the following
error messages:
[luchtan@mango luchtan]$ ga GUS::Common::Plugin::LoadPfam --release=8.0
--flat_file=/scratch/luchtan/Pfam-A.full --verbose
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/.gus.properties
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
prepareAndExecute: SELECT *
FROM Core.AlgorithmImplementation
WHERE executable = 'GUS::Common::Plugin::LoadPfam'
AND cvs_revision = '1.8b'
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t,
Core.DatabaseInfo d where d.database_id = t.database_id
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
RetrieveFromDB: select * from Core.AlgorithmImplementation where
algorithm_implementation_id = ?
bindValues (102)
prepareAndExecute: select login,user_id from Core.UserInfo
prepareAndExecute: select name,group_id from Core.GroupInfo
prepareAndExecute: select name,project_id from Core.ProjectInfo
sqlExec:
INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_id,
user_write, group_write, cpu_time, algorithm_implementation_id,
row_project_id, algorithm_invocation_id, comment_string, group_read,
row_group_id, result, other_read, cpus_used, start_time,
modification_date, user_read, row_alg_invocation_id, other_write,
machine_id )
VALUES ( SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, SYSDATE,
SYSDATE, ?, ?, ?, ? )
bindValues (6, 1, 1, 0, 102, 2, 229, 1, 3, pending, 1, 1, 1, 1, 0, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
getRelations: select * from Core.AlgorithmParamKey where
algorithm_implementation_id = ?
bindValues (102)
getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
bindValues (2)
sqlExec:
INSERT INTO Core.AlgorithmParam ( row_user_id, user_write,
group_write, is_default, order_num, row_project_id, int_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
)
bindValues (6, 1, 1, 0, 0, 2, 1, 229, 1, 1, 3, 1, 1, 229, 2483, 474, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
bindValues (0)
sqlExec:
INSERT INTO Core.AlgorithmParam ( row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2484, 480, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
getRelations: select * from Core.AlgorithmParamKeyType where
algorithm_param_key_type_id = ?
bindValues (4)
sqlExec:
INSERT INTO Core.AlgorithmParam ( row_user_id, user_write,
group_write, is_default, order_num, row_project_id, boolean_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2485, 479, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
sqlExec:
INSERT INTO Core.AlgorithmParam ( row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (6, 1, 1, 0, 0, 2, 229, 1, /scratch/luchtan/Pfam-A.full, 3,
1, 1, 229, 2486, 477, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
sqlExec:
INSERT INTO Core.AlgorithmParam ( row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2487, 473, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
sqlExec:
INSERT INTO Core.AlgorithmParam ( row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (6, 1, 1, 0, 0, 2, 229, 1, /home/luchtan/.gus.properties, 3,
1, 1, 229, 2488, 476, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
sqlExec:
INSERT INTO Core.AlgorithmParam ( row_user_id, user_write,
group_write, is_default, order_num, row_project_id, boolean_value,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
? )
bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2489, 482, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
sqlExec:
INSERT INTO Core.AlgorithmParam ( row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2490, 481, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
sqlExec:
INSERT INTO Core.AlgorithmParam ( row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (6, 1, 1, 0, 0, 2, 229, 1, 8.0, 3, 1, 1, 229, 2491, 475, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
sqlExec:
INSERT INTO Core.AlgorithmParam ( row_user_id, user_write,
group_write, is_default, order_num, row_project_id,
algorithm_invocation_id, group_read, string_value, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_id, algorithm_param_key_id, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (6, 1, 1, 0, 0, 2, 229, 1, 3, 1, 1, 229, 2492, 478, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
ImportPfam: COMMIT OFF
ImportPfam: reading Pfam release 8.0 from /scratch/luchtan/Pfam-A.full
In readExternalDbReleases()
0: PF00244
sqlExec:
INSERT INTO DoTS.PfamEntry ( row_user_id, alignment_method,
user_write, group_write, accession, row_project_id, group_read,
row_group_id, other_read, release, modification_date, user_read,
number_of_seqs, pfam_entry_id, row_alg_invocation_id, author, definition,
identifier, other_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?,
?, ? )
bindValues (6, Clustalw, 1, 1, PF00244, 2, 1, 3, 1, 8.0, 1, 203, 9, 229,
Finn RD, 14-3-3 protein, 14-3-3, 0)
DbiHandle:sqlExec:insert succeeded 1 row(s)
sqlExec:
UPDATE Core.AlgorithmInvocation
SET
end_time = SYSDATE,
row_alg_invocation_id = ?,
modification_date = SYSDATE
WHERE algorithm_invocation_id = ?
bindValues (229, 229)
DbiHandle:sqlExec:insert succeeded 1 row(s)
Unable to find ID for ExternalDatabase medline at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm line 414, <PFAM>
line 493.
***********************************************
My first thought was to add an entry to the sres.externaldatabase table
like so:
insert into Sres.Externaldatabase
values(95,'medline','medline',SYSDATE,1,1,1,1,1,0,6,3,2,1);
But even after doing so I get the same error.
Does anyone have any ideas?
Michael Luchtan
http://www.cs.uga.edu/~luchtan
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