[Bioperl-l] One more load_seqdatabase.pl question

gang wu gwu at molbio.mgh.harvard.edu
Tue Nov 28 16:13:11 EST 2006


Hi everyone,

I'm using load_seqdatabase.pl to upload some Genbank genome sequences to 
my Oracle BioSQL database. I saw some errors(See attached warning 
message) related to seqfeature_qualifier_value 
(SG_SEQFEATURE_QUALIFIER_ASSOC.VALUE column), which has Varchar2 data 
type of maximum 4000 bytes. Did anybody mention this issue before? 
Should I just modify the column to a type being able store more data 
such as LONG or CLOB?

Thanks.

Gang


Log information:
============================================

load_seqdatabase.pl -host elegans -driver Oracle -dbname sparc -dbuser 
biosqldb-sgowner -dbpass PASS -format genbank -namespace genbank 
/genomeseq/arabidopsis//NC_003070.gbk


Loading /genomeseq/arabidopsis//NC_003070.gbk ...


-------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement 
execution: ORA-01461: can bind a LONG value only for insert into a LONG 
column (DBD ERROR: error possibly near <*> indicator at char 12 in 
'INSERT INTO <*>seqfeature_qualifier_value (fea_oid, trm_oid, value, 
rank) VALUES (:p1, :p2, :p3, :p4)')
    name: INSERT ASSOC [2] 
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
    values: FK[Bio::SeqFeature::Generic]:14898, 
FK[Bio::Annotation::SimpleValue]:800, 
value:"MVAVTGEVLHLLRRYLGEYVHGLSTEALRISVWKGDVVLKDLKLKAEALNSLKLPVAVKSGFVGTITLKVPWKSLGKEPVIVLIDRVFVLAYPAPDDRTLKFFTLVGTEFAYTNYIPGGRQGKASRNQASADRGTSYFWLMELHGYEAETATLEARAKSKLGSPPQGNSWLGSIIATIIGNLKVSISNVHIRYEDSTRDSSEILASFFSYFNNICSSNPGHPFAAGITLAKLAAVTMDEEGNETFDTSGALDKLRKSLQLERLALYHDSNSFPWEIEKQWDNITPEEWIEMFEDGIKEQTEHKIKSKWALNRHYLLSPINGSLKYHRLGNQERNNPEIPFERASVILNDVNVTITEEQYHDWIKLVEVVSRYKTYIEISHLRPMVPVSEAPRLWWRFAAQASLQQKRLWYTRYIQLYANFLQQSSDVNYPEMREIEKDLDSKVILLWRLLAHAKVESVKSKEAAEQRKLKKGGWFSFNWRTEAEDDPEVDSVAGGSKLMEERLTKDEWKAINKLLSHQPDEEMNLYSGKDMQNMTHFLVTVSIGQGAARIVDINQTEVLCGRFEQLDVTTKFRHRSTQCDVSLRFYGLSAPEGSLAQSVSSERKTNALMASFVNAPIGENIDWRLSATISPCHATIWTESYDRVLEFVKRSNAVSPTVALETAAVLQMKLEEVTRRAQEQLQIVLEEQSRFALDIDIDAPKVRIPLRASGSSKCSSHFLLDFGNFTLTTMDTRSEEQRQNLYSRFCISGRDIAAFFTDCGSDNQGCSLVMEDFTNQPILSPILEKADNVYSLIDRCGMAVIVDQIKVPHPSYPSTRISIQVPNIGVHFSPTRYMRIMQLFDILYGAMKTYSQAPVDHMPDGIQPWSPTDLASDARILVWKGIGNSVATWQSCRLVLSGLYLYTFESEKSLDYQRYLCMAGRQVFEVPPANIGGSPYCLAVGVRGTDLKKALESSSTWIIEFQGEEKAAWLRGLVQATYQASAPLSGDVLGQTSDGDGDFHEPQTRNMKAADLVITGALVETKLYLYGKIKNECDEQVEEVLLLKVLASGGKVHLISSESGLTVRTKLHSLKIKDELQQQQSGSAQYLAYSVLKNEDIQESLGTCDSFDKEMPVGHADDEDAYTDALPEFLSPTEPGTPDMDMIQCSMMMDSDEHVGLEDTEGGFHEKDTSQGKSLCDEVFYEVQGGEFSDFVSVVFLTRSSSSHDYNGIDTQMSIRMSKLEFFCSRPTVVALIGFGFDLSTASYIENDKDANTLVPEKSDSEKETNDESGRIEGLLGYGKDRVVFYLNMNVDNVTVFLNKEDGSQLAMFVQERFVLDIKVHPSSLSVEGTLGNFKLCDKSLDSGNCWSWLCDIRDPGVESLIKFKFSSYSAGDDDYEGYDYSLSGKLSAVRIVFLYRFVQEVTAYFMGLATPHSEEVIKLVDKVGGFEWLIQKDEMDGATAVKLDLSLDTPIIVVPRDSLSKDYIQLDLGQLEVSNEISWHGCPEKDATAVRVDVLHAKILGLNMSVGINGSIGKPMIREGQGLDIFVRRSLRDVFKKVPTLSVEVKIDFLHAVMSDKEYDIIVSCTSMNLFEEPKLPPDFRGSSSGPKAKMRLLADKVNLNSQMIMSRTVTILAVDINYALLELRNSVNEESSLAHVAVRASEPNSSISWMTSLSETDLYVSVPKVSVLDIRPNTKPEMRLMLGSSVDASKQASSESLPFSLNKGSFKRANSRAVLDFDAPCSTMLLMDYRWRASSQSCVLRVQQPRILAVPDFLLAVGEFFVPALRAITGRDETLDPTNDPITRSRGIVLSEPLYKQTEDVVHLSPRRQLVADSLGIDEYTYDGCGKVISLSEQGEKDLNVGRLEPIIIVGHGKKLRFVNVKIKNGSLLSKCIYLSNDSSCLFSPEDGVDISMLENASSNPENVLSNAHKSSDVSDTCQYDSKSGQSFTFEAQVVSPEFTFFDGTKSSLDDSSAVEKLLRVKLDFNFMYASKEKDIWVRALLKNLVVETGSGLIILDPVDISGGYTSVKEKTNMSLTSTDIYMHLSLSALSLLLNLQSQVTGALQSGNAIPLASCTNFDRIWVSPKENGPRNNLTIWRPQAPSNYVILGDCVTSRAIPPTQAVMAVSNTYGRVRKPIGFNRIGLFSVIQGLEGDNVQHSHNSNECSLWMPVAPVGYTAMGCVANIGSEQPPDHIVYCLSIWRADNVLGAFYAHTSTAAPSKKYSPGLSHCLLWNPLQSKTSSSSDPSSTSGSRSEQSSDQTGNSSGWDILRSISKATSYHVSTPNFERIWWDKGGDLRRPVSIWRPVPRPGFAILGDSITEGLEPPALGILFKADDSEIAAKPVQFNKVAHIVGKGFDEVFCWFPVAPPGYVSLGCVLSKFDEAPHVDSFCCPRIDLVNQANIYEASVTRSSSSKSSQLWSIWKVDNQACTFLARSDLKRPPSRMAFAVGESVKPKTQENVNAEIKLRCFSLTLLDGLHGMMTPLFDTTVTNIKLATHGRPEAMNAVLISSIAASTFNPQLEAWEPLLEPFDGIFKLETYDTALNQSSKPGKRLRIAATNILNINVSAANLETLGDAVVSWRRQLELEERAAKMKEESAASRESGDLSAFSALDEDDFQTIVVENKLGRDIYLKKLEENSDVVVKLCHDENTSVWVPPPRFSNRLNVADSSREARNYMTVQILEAKGLHIIDDGNSHSFFCTLRLVVDSQGAEPQKLFPQSARTKCVKPSTTIVNDLMECTSKWNELFIFEIPRKGVARLEVEVTNLAAKAGKGEVVGSLSFPVGHGESTLRKVASVRMLHQSSDAENISSYTLQRKNAEDKHDNGCLLISTSYFEKTTIPNTLRNMESKDFVDGDTGFWIGVRPDDSWHSIRSLLPLCIAPKSLQNDFIAMEVSMRNGRKHATFRCLATVVNDSDVNLEISISSDQNVSSGVSNHNAVIASRSSYVLPWGCLSKDNEQCLHIRPKVENSHHSYAWGYCIAVSSGCGKDQPFVDQGLLTRQNTIKQSSRASTFFLRLNQLEKKDMLFCCQPSTGSKPLWLSVGADASVLHTDLNTPVYDWKISISSPLKLENRLPCPVKFTVWEKTKEGTYLERQHGVVSSRKSAHVYSADIQRPVYLTLAVHGGWALEKDPIPVLDISSNDSVSSFWFVHQQSKRRLRVSIERDVGETGAAPKTIRFFVPYWITNDSYLPLSYRVVEIEPSENVEAGSPCLTRASKSFKKNPVFSMERRHQKKNVRVLESIEDTSPMPSMLSPQESAGRSGVVLFPSQKDSYVSPRIGIAVAARDSDSYSPGISLLELEKKERIDVKAFCKDASYYMLSAVLNMTSDRTKVIHLQPHTLFINRVGVSICLQQCDCQTEEWINPSDPPKLFGWQSSTRLELLKLRVKGYRWSTPFSVFSEGTMRVPVPKEDGTDQLQLRVQVRSGTKNSRYEVIFRPNSISGPYRIENRSMFLPIRYRQVEGVSESWQFLPPNAAASFYWENLGRRHLFELLVDGNDPSNSEKFDIDKIGDYPPRSESGPTRPIRVTILKEDKKNIVRISDWMPAIEPTSSISRRLPASSLSELSGNESQQSHLLASEDSEFHVIVELAELGISVIDHAPEEILYMSVQNLFVAYSTGLGSGLSRFKLRMQGIQVDNQLPLAPMPVLFRPQRTGDKADYILKFSVTLQSNAGLDLRVYPYIDFQGRENTAFLINIHEPIIWRIHEMIQQANLSRLSDPNSTAVSVDPFIQIGVLNFSEVRFRVSMAMSPSQRPRGVLGFWSSLMTALGNTENMPVRISERFHENISMRQSTMINNAIRNVKKDLLGQPLQLLSGVDILGNASSALGHMSQGIAALSMDKKFIQSRQRQENKGVEDFGDIIREGGGALAKGLFRGVTGILTKPLEGAKSSGVEGFVSGFGKGIIGAAAQPVSGVLDLLSKTTEGANAMRMKIAAAITSDEQLLRRRLPRAVGADSLLRPYNDYRAQGQVILQLAESGSFLGQVDLFKVRGKFALTDAYESHFILPKGKVLMITHRRVILLQQPSNIMGQRKFIPAKDACSIQWDILWNDLVTMELSDGKKDPPNSPPSRLILYLKAKPHDPKEQFRVVKCIPNSKQAFDVYSAIDQAINLYGQNALKGMVKNKVTRPYSPISESSWAEGASQQMPASVTPSSTFGTSPTTSSS", 
rank:"1"
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