[Bioperl-l] load_seqdatabase.pl error

[Forrest Zhang]

I reinstall the bioperl-db, I found some error.

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=320)
---------------------------------------------------
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, 35 wallclock secs (16.67 cusr +  0.63 csys = 17.30
CPU)
Failed 1/16 test programs. -30/1423 subtests failed.
make: *** [test] Error 255

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Forrest Zhang
Sent: Friday, September 28, 2007 11:15 AM
To: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] load_seqdatabase.pl error

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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