[Gusdev-gusdev] source_id error with LoadNRDB

[Pablo N. M. <pa...@pa...>]

Hello all,
I've been "playing" with the loadNRDB module in the previous weeks, but
it is still crashing. I got this "cannot insert NULL into source_id
(DoTS.NRDBEntry)" error when reading line 8298021 of my NR file.

That line is:
>gi|45549465|gb|AAS67649.1| spike glycoprotein S1 subunit precursor
[Avian infectious bronchitis virus]

I cannot see why this would crash. I'm looking into the code, but maybe
someone who already knows the module can help me with guesses.

Here part of the dump:

[pablo@mkiwi loadNRDB]$ ga GUS::Common::Plugin::LoadNRDB
--comment="loading NRDB data from July" --extDbRelId=48
--gitax="/home/luchtan/GUS/loadNRDB/June232004/gi_taxid_prot.dmp"
--nrdb="/scratch/pablo/nr"
--SourceDB="84:tpe,76:pdb,77:dbj,78:prf,79:emb,81:sp,82:pir,80:gb,83:ref,80:tpg,151:genpept,153:tpd" --plugin --temp_login='pablo' --temp_password='pablo123' --dbi_str='dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD' --commit | tee loadnrdb.log
(...)
Submitted set number:1462975
DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
("DOTS"."NRDBENTRY"."SOURCE_ID") (DBD ERROR: OCIStmtExecute) at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, <NRDB>
line 8298021.
 
 SQL ERROR!! involving
  
    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, user_write,
group_write, nrdb_entry_id, is_preferred, row_project_id, taxon_id,
external_database_release_id, group_read, aa_sequence_id, row_group_id,
other_read, gid, source_id, modification_date, user_read,
row_alg_invocation_id, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, '', SYSDATE,
?, ?, ? )
 Values: Luminal binding protein 3 (BiP 3) (78 kDa glucose-regulated
protein homolog 3) (GRP 78-3), 8, 1, 1, 5063019, 1, 2, 169692, 81, 1,
2943307, 2, 1, 729619, 1, 30713, 0 at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
       
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x85d0184)', '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NRDBEntry (  desc...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
       
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x85d0184)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x450007d8)', 'ARRAY(0x40a8ffd0)', '^J    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, use...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
       
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)', 'HASH(0x11e51efc)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
       
GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
       
GUS::Model::GusRow::submit('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)', undef, 1) called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
       
GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)', 'GUS::Model::DoTS::NRDBEntry') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
       
GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
       
GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)') called at /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 335
       
GUS::Common::Plugin::LoadNRDB::makeNRDBAndExternalAASequence('GUS::Common::Plugin::LoadNRDB=HASH(0x856d7c0)', 'HASH(0x85a26cc)', 'HASH(0x85a23cc)', 48) called at /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 127
       
GUS::Common::Plugin::LoadNRDB::run('GUS::Common::Plugin::LoadNRDB=HASH(0x856d7c0)', 'HASH(0x8811950)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 430
        eval {...} called at
/var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
       
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::LoadNRDB') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
       
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::LoadNRDB') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
       
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11
 
Thanks,
Pablo


-- 
-----------------------------
Pablo Nascimento Mendes
Research Scholar
Kissinger Lab
Department of Genetics
University of Georgia
C210 Life Sciences Bldg.
Athens, Georgia 30602
Phone:706 542-1447
E-mail: pa...@ug...