[Bioperl-l] 答复: load_seqdatabase.pl error

Wed Oct 24 16:00:24 UTC 2007

Dear Chris,
	I was using different swissprot data all of the have some error about the taxon.
Maybe I should re-install bioperl and biosql. Could you give me the install protocol 
what you used.

Forrest Zhang

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu] 
Sent: Wednesday, October 24, 2007 12:21 PM
To: Forrest Zhang
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] 答复: [Bioperl-l] load_seqdatabase.pl error

Forrest, it's working fine for me (no warnings):

cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe -- 
namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** -- 
format swiss Q40784.txt
Loading Q40784.txt ...
cjfields:~/tests/db_tests cjfields$

That was the sequence that failed (Q40784) and the format (swiss) you  
used, correct?

chris

On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:

> Dear Chris:
> 	What's the result of test? In my computer, the test haven't been
> passed.
>
> Forrest Zhang
>
> -----邮件原件-----
> 发件人: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] 代表 Chris Fields
> 发送时间: 2007年9月29日 6:03
> 收件人: Forrest Zhang
> 抄送: bioperl-l at bioperl.org BioPerl
> 主题: 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
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> 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