[Bioperl-l] =?gb2312?B?tPC4tDogW0Jpb3BlcmwtbF0gbG9hZF9zZXFkYXRhYmFzZS5wbCBlcnJvcg==?=

Forrest Zhang forrest_zhang at 163.com
Tue Oct 23 23:27:00 EDT 2007


Dear Chris:
	What's the result of test? In my computer, the test haven't been
passed.

Forrest Zhang

-----ÓʼþÔ­¼þ-----
·¢¼þÈË: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] ´ú±í Chris Fields
·¢ËÍʱ¼ä: 2007Äê9ÔÂ29ÈÕ 6:03
ÊÕ¼þÈË: Forrest Zhang
³­ËÍ: bioperl-l at bioperl.org BioPerl
Ö÷Ìâ: Re: [Bioperl-l] load_seqdatabase.pl error

Okay, fixed the recursion (extra copy of a BasePersistentAdaptor  
module I was working which tripped it, so nothing in CVS).

Forrest, I get all tests passing.  I used a database without taxonomy  
loaded with bioperl-db and bioperl from cvs and it worked w/o  
problems.  I'll try working with your sequence when I have time this  
weekend.

chris

On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:

> I'm actually getting some odd recursion issues again; not sure what's
> causing it, but a reinstall of both bioperl and bioperl-db fixed it
> last time.  It may be related to the rollback, just not sure yet.
>
> I'll try tracking it down if it persists (bad pun).
>
> t/04swiss....ok 3/52
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
> t/04swiss....ok
> All tests successful.
> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
> CPU)
>
> The specific error under verbose running is:
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:680
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:691
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:691
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:658
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:252
> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> PrimarySeqAdaptor.pm:229
> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/src/
> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:213
> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:244
> STACK toplevel t/04swiss.t:37
> ---------------------------------------------------
>
>
> chris
>
> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>
>> 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 :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> 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 :
>> ===========================================================
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign



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