[Bioperl-l] load_seqdatabase.pl error

Forrest Zhang forrest_zhang at 163.com
Fri Sep 28 07:28:41 EDT 2007


Message using CVS.

biocc bioperl-db # ./Build test
Copying scripts/biosql/terms/importrelation.pl ->
blib/script/importrelation.pl
blib/script/importrelation.pl -> blib/script/bp_importrelation.pl
Copying scripts/biosql/merge-unique-ann.pl ->
blib/script/merge-unique-ann.pl
blib/script/merge-unique-ann.pl -> blib/script/bp_merge-unique-ann.pl
Copying scripts/biosql/update-on-new-date.pl ->
blib/script/update-on-new-date.pl
blib/script/update-on-new-date.pl -> blib/script/bp_update-on-new-date.pl
Copying scripts/biosql/terms/add-term-annot.pl ->
blib/script/add-term-annot.pl
Deleting blib/script/add-term-annot.pl.bak
blib/script/add-term-annot.pl -> blib/script/bp_add-term-annot.pl
Copying scripts/corba/caching_corba_server.pl ->
blib/script/caching_corba_server.pl
Deleting blib/script/caching_corba_server.pl.bak
blib/script/caching_corba_server.pl ->
blib/script/bp_caching_corba_server.pl
Copying scripts/biosql/load_ontology.pl -> blib/script/load_ontology.pl
Deleting blib/script/load_ontology.pl.bak
blib/script/load_ontology.pl -> blib/script/bp_load_ontology.pl
Copying scripts/biosql/load_seqdatabase.pl ->
blib/script/load_seqdatabase.pl
Deleting blib/script/load_seqdatabase.pl.bak
blib/script/load_seqdatabase.pl -> blib/script/bp_load_seqdatabase.pl
Copying scripts/biosql/terms/interpro2go.pl -> blib/script/interpro2go.pl
blib/script/interpro2go.pl -> blib/script/bp_interpro2go.pl
Copying scripts/biosql/clean_ontology.pl -> blib/script/clean_ontology.pl
blib/script/clean_ontology.pl -> blib/script/bp_clean_ontology.pl
Copying scripts/corba/test_bioenv.pl -> blib/script/test_bioenv.pl
Deleting blib/script/test_bioenv.pl.bak
blib/script/test_bioenv.pl -> blib/script/bp_test_bioenv.pl
Copying scripts/biosql/update-on-new-version.pl ->
blib/script/update-on-new-version.pl
blib/script/update-on-new-version.pl ->
blib/script/bp_update-on-new-version.pl
Copying scripts/biosql/bioentry2flat.pl -> blib/script/bioentry2flat.pl
Deleting blib/script/bioentry2flat.pl.bak
blib/script/bioentry2flat.pl -> blib/script/bp_bioentry2flat.pl
Copying scripts/corba/bioenv_server.pl -> blib/script/bioenv_server.pl
Deleting blib/script/bioenv_server.pl.bak
blib/script/bioenv_server.pl -> blib/script/bp_bioenv_server.pl
Copying scripts/biosql/load_interpro.pl -> blib/script/load_interpro.pl
blib/script/load_interpro.pl -> blib/script/bp_load_interpro.pl
Copying scripts/biosql/cgi-bin/getentry.pl -> blib/script/getentry.pl
Deleting blib/script/getentry.pl.bak
blib/script/getentry.pl -> blib/script/bp_getentry.pl
Copying scripts/biosql/del-assocs-sql.pl -> blib/script/del-assocs-sql.pl
blib/script/del-assocs-sql.pl -> blib/script/bp_del-assocs-sql.pl
Copying scripts/biosql/freshen-annot.pl -> blib/script/freshen-annot.pl
blib/script/freshen-annot.pl -> blib/script/bp_freshen-annot.pl
t/01dbadaptor.....ok

t/02species.......FAILED tests 66-95

        Failed 30/65 tests, 53.85% okay
t/03simpleseq.....ok

t/04swiss.........ok

t/05seqfeature....ok

t/06comment.......ok

t/07dblink........ok

t/08genbank.......ok

t/09fuzzy2........ok

t/10ensembl.......ok

t/11locuslink.....ok

t/12ontology......ok

t/13remove........ok

t/14query.........ok

t/15cluster.......ok 9/160

--------------------- WARNING ---------------------
MSG: failed to store one or more child objects for an instance of class
Bio::Cluster::UniGene (PK=366)
---------------------------------------------------
t/15cluster.......ok

t/16obda..........ok

Failed Test   Stat Wstat Total Fail  List of Failed
----------------------------------------------------------------------------
---
t/02species.t               65   30  66-95
Failed 1/16 test scripts. -30/1423 subtests failed.
Files=16, Tests=1423, 36 wallclock secs (16.64 cusr +  0.65 csys = 17.29
CPU)
Failed 1/16 test programs. -30/1423 subtests failed.

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Friday, September 28, 2007 1:00 PM
To: Forrest Zhang
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] load_seqdatabase.pl error

If this is occurring using bioperl from CVS then I'll try taking a  
look at it.

chris

On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:

> Hilmar,
> 	I have already pre-loaded the NCBI taxonomy using
> load_ncbi_taxonomy.pl yet. The error message show:
>
> --------------------- WARNING ---------------------
> MSG: The supplied lineage does not start near 'Phaseolus aureus' (I  
> was
> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I  
> | rosids
> | core eudicotyledons | eudicotyledons | Magnoliophyta |  
> Euphyllophyta |
> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
> ---------------------------------------------------
> Could not store Q40784:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Species) failed to insert or to be found  
> by unique
> key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::Persistent::PersistentObject::create
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/ 
> PersistentObject.pm:244
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:169
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/ 
> PersistentObject.pm:271
> STACK: /usr/bin/bp_load_seqdatabase.pl:633
> -----------------------------------------------------------
> Sigh~~~~~~
>
> Forrest Zhang
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: Friday, September 28, 2007 6:17 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest,
>
> have you preloaded the NCBI taxonomy as suggested in the BioSQL
> installation guidelines? SwissProt format has NCBI taxon IDs, and the
> code will try to use it to look up species and their lineage, rather
> than inserting the lineage from whatever BioPerl parses out of the
> sequence record.
>
> 	-hilmar
>
> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>
>> Hi, all
>>     I install the biosql, and bioperl-db. I want to import
>> swissport data.
>> But the programe show some error as below:
>> ===================================================================== 
>> =
>> ======
>> ===============================================
>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver mysql
>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>> Could not store Q6DAH5:
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>> subsp.
>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>> Pectobacterium |
>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>> Proteobacteria | Bacteria')
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>> STACK: Bio::Species::classification
>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>> PersistentObject.pm:552
>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:1305
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:973
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:852
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:182
>> STACK: Bio::DB::Persistent::PersistentObject::create
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>> PersistentObject.pm:244
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:169
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:251
>> STACK: Bio::DB::Persistent::PersistentObject::store
>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>> PersistentObject.pm:271
>> STACK: load_seqdatabase.pl:620
>> -----------------------------------------------------------
>>
>>  at load_seqdatabase.pl line 633
>> ===================================================================== 
>> =
>> ======
>> ===============================================
>>
>> How can I solve it, please help me, Thank you.
>>
>> Thanks
>> Forrest zhang
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
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> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign



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