Re: [Gusdev-gusdev] source_id error with LoadNRDB

[Deborah F. P. <pi...@pc...>]

Hi,

I've had some hard to track down problems with entries in the nr protein 
db. Several of these were due to new undocumented source databases - I 
don't think NCBI supports this database as far as documentation goes (they 
don't keep it up to date) although they do update the files very 
frequently, I think nightly. The last time I loaded, they had violated the 
format by neglecting to put the ^A before a subsequent entry in the 
defline, something I could see by opening the file using vi. I think I 
got the error you are getting.

I can't really check this entry in the files I have because I don't think 
the line you sent is the one in question, based on the description. (spike 
glycoprotein S1 subunit precursor... vs Luminal binding protein 3...).


If you encountered this error after successfully loading many others than 
I would suspect some problem with the entry itself.

                                                       Debbie


On Thu, 5 Aug 2004, Pablo N. Mendes wrote:

> 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...
>
>
>
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