[Bioperl-l] load_seqdatabase.pl error

Chris Fields cjfields at uiuc.edu
Fri Sep 28 16:10:59 UTC 2007 

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

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