[Bioperl-l] load_seqdatabase.pl error

Hilmar Lapp hlapp at gmx.net
Fri Sep 28 11:53:33 EDT 2007


Chris let me know if you get stumped. I'm surprised that the special  
ranks ('eurosids I' etc) show up in the lineage (has NCBI started to  
assign ranks to them? I thought I filter them out. Needs to be looked  
into too.), but at any rate I don't understand why they aren't being  
accepted.

Also, maybe we need a more verbose output here - Forrest, can you run  
this with adding a --printerror argument. (I'm embarrassed to find  
that this doesn't seem to be documented. Sigh.)

	-hilmar

On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:

> 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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>>
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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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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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