[Bioperl-l] FW: FW: 答复: load_seqdatabase.pl error

Forrest Zhang forrest_zhang at 163.com
Fri Oct 26 04:21:56 EDT 2007


Chris,
	I am using --safe to loading sequence. Maybe I would load species data one by one.
It seem be OK now.

	Thanks for your help so much Chris.

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 Chris Fields
Sent: Thursday, October 25, 2007 9:07 PM
To: Forrest Zhang; BioSQL
Cc: bioperl-l at bioperl.org BioPerl
Subject: Re: [Bioperl-l] FW: 答复: load_seqdatabase.pl error

Forrest,

I'm cross-posting this to BioSQL.  Maybe you can get more response  
there (I'm not the best person to ask about bioperl-db).

BioSQL can be found here:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/

The 'table x is full' probably has to do with the second (more  
critical) error, that being the sequence may already appears in the  
database ('failed to insert or be found by unique key').  Are you  
loading sequences  using --safe mode?

chris

On Oct 25, 2007, at 3:16 AM, Forrest Zhang wrote:

> Chris,
> 	Faint, the other kind error about "The table 'reference' is full"  
> when I was loading uniprot_sprot_human data.
> 	Maybe the biosqldb-mysql.sql of my downloaded have some bugs.  
> Where can I download the appropriate version?
>
>
> Loading uniprot_sprot_human.dat ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
> values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich  
> P.C., Hermanns H.M.",""Characterization of the signaling capacities  
> of the novel gp130-like cytokine receptor."","J. Biol. Chem.  
> 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
> The table 'reference' is full
> ---------------------------------------------------
> Could not store Q8NI17:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Annotation::Reference) 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:359
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
> 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:  
> Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/ 
> lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> AnnotationCollectionAdaptor.pm:217
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> 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: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> 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:623
> -----------------------------------------------------------
>
>  at /usr/bin/bp_load_seqdatabase.pl line 636
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Thursday, October 25, 2007 12:48 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] 答复: load_seqdatabase.pl error
>
> I use the exact procedure on the web site using Build.PL, just using
> bioperl-live and bioperl-db:
>
> http://www.bioperl.org/wiki/
> Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_.
> 27Build.PL.27
>
> You may have some tests fail, but >98% should pass (if not all of
> them).  Install anyway.
>
> Prior to the bioperl-db tests I loaded a database with the BioSQL
> schema, then just ran:
>
> perl Build.PL
> ./Build
> ./Build test
> ./Build install
>
> with the proper configuration; everything passes, with one warning
> for Unigene I think (which is normal).  I install taxonomy afterwards.
>
> One thing to note: make sure you do not have multiple bioperl
> versions installed (either db or live).  Note where the above distros
> install and then check which version is being used by using:
>
> perldoc -l 'Bio::Root::Root'
>
> If it isn't pointing at the same install directory then perl is using
> another BioPerl installation elsewhere in @INC, which needs to be
> removed.
>
> chris
>
> On Oct 24, 2007, at 11:00 AM, Forrest wrote:
>
>> 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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>
>
>
>
> _______________________________________________
> 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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