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

Forrest Zhang forrest_zhang at 163.com
Thu Oct 25 08:16:34 UTC 2007 


-----Original Message-----
From: Forrest Zhang [mailto:forrest_zhang at 163.com] 
Sent: Thursday, October 25, 2007 4:16 PM
To: 'Chris Fields'
Subject: RE: [Bioperl-l] 答复: load_seqdatabase.pl error

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

More information about the Bioperl-l mailing list