[Gmod-schema] a question of loading data into chado database

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[Gmod-schema] a question of loading data into chado database

zhuang chao
When I was loading the gff3 file into chado database using gmod_bulk_load_gff3.pl, I got  the errors like this:

DBD::Pg::db commit failed: ERROR:  insert or update on table
"feature_relationship" violates foreign key constraint
"feature_relationship_subject_id_fkey"
DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
line 41.

commit failed: ERROR:  insert or update on table "feature_relationship"
violates foreign key constraint "feature_relationship_subject_id_fkey"
DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
line 41.

I don't know why and how to handle. Could you help me?
I am looking forward to your reply.  Thank you very much !
 
--------------
zhuangchao
2010-05-18



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Re: [Gmod-schema] a question of loading data into chado database

Scott Cain
Hi zhuangchao,

Are you using Chado from the 1.0 release or from svn?  I believe that
people have had that problem with the 1.0 release but it is fixed in
svn.  You can get Chado from svn by following these directions and
checking out the schema repository:

  http://gmod.org/wiki/SVN

(As a side note, I've promised myself to get the 1.1 release out this week.)

If you are already using Chado from svn, please give us more
information, like a sample of GFF that causes the problem, and perhaps
a history of how you've loaded previous data (if you have).  Finally,
you might want to use the option --save_tmpfiles and examine them for
where in the GFF file the missing feature would have occurred that the
database is complaining that it doesn't exist.

Scott


On Tue, May 18, 2010 at 2:54 AM, 庄超 <[hidden email]> wrote:

> When I was loading the gff3 file into chado database using gmod_bulk_load_gff3.pl, I got  the errors like this:
>
> DBD::Pg::db commit failed: ERROR:  insert or update on table
> "feature_relationship" violates foreign key constraint
> "feature_relationship_subject_id_fkey"
> DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
> at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
> line 41.
>
> commit failed: ERROR:  insert or update on table "feature_relationship"
> violates foreign key constraint "feature_relationship_subject_id_fkey"
> DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
> at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
> line 41.
>
> I don't know why and how to handle. Could you help me?
> I am looking forward to your reply.  Thank you very much !
>
> --------------
> zhuangchao
> 2010-05-18
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: a question of loading data into chado database

zhuang chao
On Tue, 2010-05-18 at 09:07 -0400, Scott Cain wrote:

> Hi zhuangchao,
>
> Are you using Chado from the 1.0 release or from svn?  I believe that
> people have had that problem with the 1.0 release but it is fixed in
> svn.  You can get Chado from svn by following these directions and
> checking out the schema repository:
>
>   http://gmod.org/wiki/SVN
>
> (As a side note, I've promised myself to get the 1.1 release out this week.)
>
> If you are already using Chado from svn, please give us more
> information, like a sample of GFF that causes the problem, and perhaps
> a history of how you've loaded previous data (if you have).  Finally,
> you might want to use the option --save_tmpfiles and examine them for
> where in the GFF file the missing feature would have occurred that the
> database is complaining that it doesn't exist.
>
> Scott
>
>
> On Tue, May 18, 2010 at 2:54 AM, 庄超 <[hidden email]> wrote:
> > When I was loading the gff3 file into chado database using gmod_bulk_load_gff3.pl, I got  the errors like this:
> >
> > DBD::Pg::db commit failed: ERROR:  insert or update on table
> > "feature_relationship" violates foreign key constraint
> > "feature_relationship_subject_id_fkey"
> > DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
> > line 41.
> >
> > commit failed: ERROR:  insert or update on table "feature_relationship"
> > violates foreign key constraint "feature_relationship_subject_id_fkey"
> > DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
> > line 41.
> >
> > I don't know why and how to handle. Could you help me?
> > I am looking forward to your reply.  Thank you very much !
> >
> > --------------
> > zhuangchao
> > 2010-05-18
> >
> >
> >
> > ------------------------------------------------------------------------------
> >
> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >
>
>
>



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Re: a question of loading data into chado database

zhuang chao
In reply to this post by zhuang chao
hello , Scott

I   downloaded    Chado from svn . But  the question still  exist .

The   gff file   is  in  the  attachment  . Here  is     a  history of

 how I  loaded previous data  .   Thank  you very much !

===============================================
root@bnode6:/home/zc/Download#
perl /usr/local/bin/gmod_bulk_load_gff3.pl  --gfffile     NC_001437.gff
--organism 'Japanese encephalitis virus' --dbname four_viruses  --dbuser
zc --dbpass 123456 --dbhost localhost --dbport 5432  --save_tmpfiles


Preparing data for inserting into the four_viruses database
(This may take a while ...)
Dropping cds temp tables...
Creating cds temp tables...
NOTICE:  CREATE TABLE will create implicit sequence
"tmp_cds_handler_cds_row_id_seq" for serial column
"tmp_cds_handler.cds_row_id"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"tmp_cds_handler_pkey" for table "tmp_cds_handler"
NOTICE:  CREATE TABLE will create implicit sequence
"tmp_cds_handler_relationship_rel_row_id_seq" for serial column
"tmp_cds_handler_relationship.rel_row_id"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"tmp_cds_handler_relationship_pkey" for table
"tmp_cds_handler_relationship"


There are both CDS and exon features in this file, but
you did not set the --noexon option, which you probably want.
Please see `perldoc gmod_bulk_load_gff3.pl for more information.

Loading data into feature table ...
Loading data into featureloc table ...
Loading data into feature_relationship table ...
Loading data into featureprop table ...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into dbxref table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Loading data into cvterm table ...
Loading data into db table ...
Skipping cv table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping organism table since the load file is empty...
DBD::Pg::db commit failed: ERROR:  insert or update on table
"feature_relationship" violates foreign key constraint
"feature_relationship_subject_id_fkey"
DETAIL:  Key (subject_id)=(66) is not present in table "feature".
at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh>
line 5.
commit failed: ERROR:  insert or update on table "feature_relationship"
violates foreign key constraint "feature_relationship_subject_id_fkey"
DETAIL:  Key (subject_id)=(66) is not present in table "feature".
at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh>
line 5.

Abnormal termination, trying to clean up...

Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...
Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting...
=======================================================



On Tue, 2010-05-18 at 09:07 -0400, Scott Cain wrote:

> Hi zhuangchao,
>
> Are you using Chado from the 1.0 release or from svn?  I believe that
> people have had that problem with the 1.0 release but it is fixed in
> svn.  You can get Chado from svn by following these directions and
> checking out the schema repository:
>
>   http://gmod.org/wiki/SVN
>
> (As a side note, I've promised myself to get the 1.1 release out this week.)
>
> If you are already using Chado from svn, please give us more
> information, like a sample of GFF that causes the problem, and perhaps
> a history of how you've loaded previous data (if you have).  Finally,
> you might want to use the option --save_tmpfiles and examine them for
> where in the GFF file the missing feature would have occurred that the
> database is complaining that it doesn't exist.
>
> Scott
>
>
> On Tue, May 18, 2010 at 2:54 AM, 庄超 <[hidden email]> wrote:
> > When I was loading the gff3 file into chado database using gmod_bulk_load_gff3.pl, I got  the errors like this:
> >
> > DBD::Pg::db commit failed: ERROR:  insert or update on table
> > "feature_relationship" violates foreign key constraint
> > "feature_relationship_subject_id_fkey"
> > DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
> > line 41.
> >
> > commit failed: ERROR:  insert or update on table "feature_relationship"
> > violates foreign key constraint "feature_relationship_subject_id_fkey"
> > DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
> > line 41.
> >
> > I don't know why and how to handle. Could you help me?
> > I am looking forward to your reply.  Thank you very much !
> >
> > --------------
> > zhuangchao
> > 2010-05-18
> >
> >
> >
> > ------------------------------------------------------------------------------
> >
> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >
>
>
>

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Re: a question of loading data into chado database

Scott Cain
Hi zhuangchao,

I just tried loading this GFF file into my Chado instance and it
loaded fine (although I supplied the --noexon flag as suggested by the
loader, but I don't think that should matter).  I see that the subject
ID that it is complaining of not existing is fairly low: is there
another GFF file that you loaded first?  I'm wondering if there is
some bad interaction between them (there shouldn't be, so that would
consitute a bug).  If there is one other GFF file, can you send that
too?

Thanks,
Scott


2010/5/19 zhuangchao <[hidden email]>:

> hello , Scott
>
> I   downloaded    Chado from svn . But  the question still  exist .
>
> The   gff file   is  in  the  attachment  . Here  is     a  history of
>
>  how I  loaded previous data  .   Thank  you very much !
>
> ===============================================
> root@bnode6:/home/zc/Download#
> perl /usr/local/bin/gmod_bulk_load_gff3.pl  --gfffile     NC_001437.gff
> --organism 'Japanese encephalitis virus' --dbname four_viruses  --dbuser
> zc --dbpass 123456 --dbhost localhost --dbport 5432  --save_tmpfiles
>
>
> Preparing data for inserting into the four_viruses database
> (This may take a while ...)
> Dropping cds temp tables...
> Creating cds temp tables...
> NOTICE:  CREATE TABLE will create implicit sequence
> "tmp_cds_handler_cds_row_id_seq" for serial column
> "tmp_cds_handler.cds_row_id"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "tmp_cds_handler_pkey" for table "tmp_cds_handler"
> NOTICE:  CREATE TABLE will create implicit sequence
> "tmp_cds_handler_relationship_rel_row_id_seq" for serial column
> "tmp_cds_handler_relationship.rel_row_id"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "tmp_cds_handler_relationship_pkey" for table
> "tmp_cds_handler_relationship"
>
>
> There are both CDS and exon features in this file, but
> you did not set the --noexon option, which you probably want.
> Please see `perldoc gmod_bulk_load_gff3.pl for more information.
>
> Loading data into feature table ...
> Loading data into featureloc table ...
> Loading data into feature_relationship table ...
> Loading data into featureprop table ...
> Skipping feature_cvterm table since the load file is empty...
> Loading data into synonym table ...
> Loading data into feature_synonym table ...
> Loading data into dbxref table ...
> Loading data into feature_dbxref table ...
> Skipping analysisfeature table since the load file is empty...
> Loading data into cvterm table ...
> Loading data into db table ...
> Skipping cv table since the load file is empty...
> Skipping analysis table since the load file is empty...
> Skipping organism table since the load file is empty...
> DBD::Pg::db commit failed: ERROR:  insert or update on table
> "feature_relationship" violates foreign key constraint
> "feature_relationship_subject_id_fkey"
> DETAIL:  Key (subject_id)=(66) is not present in table "feature".
> at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh>
> line 5.
> commit failed: ERROR:  insert or update on table "feature_relationship"
> violates foreign key constraint "feature_relationship_subject_id_fkey"
> DETAIL:  Key (subject_id)=(66) is not present in table "feature".
> at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh>
> line 5.
>
> Abnormal termination, trying to clean up...
>
> Attempting to clean up the loader temp table (so that --recreate_cache
> won't be needed)...
> Trying to remove the run lock (so that --remove_lock won't be needed)...
> Exiting...
> =======================================================
>
>
>
> On Tue, 2010-05-18 at 09:07 -0400, Scott Cain wrote:
>> Hi zhuangchao,
>>
>> Are you using Chado from the 1.0 release or from svn?  I believe that
>> people have had that problem with the 1.0 release but it is fixed in
>> svn.  You can get Chado from svn by following these directions and
>> checking out the schema repository:
>>
>>   http://gmod.org/wiki/SVN
>>
>> (As a side note, I've promised myself to get the 1.1 release out this week.)
>>
>> If you are already using Chado from svn, please give us more
>> information, like a sample of GFF that causes the problem, and perhaps
>> a history of how you've loaded previous data (if you have).  Finally,
>> you might want to use the option --save_tmpfiles and examine them for
>> where in the GFF file the missing feature would have occurred that the
>> database is complaining that it doesn't exist.
>>
>> Scott
>>
>>
>> On Tue, May 18, 2010 at 2:54 AM, 庄超 <[hidden email]> wrote:
>> > When I was loading the gff3 file into chado database using gmod_bulk_load_gff3.pl, I got  the errors like this:
>> >
>> > DBD::Pg::db commit failed: ERROR:  insert or update on table
>> > "feature_relationship" violates foreign key constraint
>> > "feature_relationship_subject_id_fkey"
>> > DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
>> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
>> > line 41.
>> >
>> > commit failed: ERROR:  insert or update on table "feature_relationship"
>> > violates foreign key constraint "feature_relationship_subject_id_fkey"
>> > DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
>> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
>> > line 41.
>> >
>> > I don't know why and how to handle. Could you help me?
>> > I am looking forward to your reply.  Thank you very much !
>> >
>> > --------------
>> > zhuangchao
>> > 2010-05-18
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> >
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>>
>>
>>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: a question of loading data into chado database

zhuang chao
hello, scott :

I supplied the  --noexon flag to load this GFF file. It was

ok  . Thank you very much !

zhuangchao


On Wed, 2010-05-19 at 09:33 -0400, Scott Cain wrote:

> Hi zhuangchao,
>
> I just tried loading this GFF file into my Chado instance and it
> loaded fine (although I supplied the --noexon flag as suggested by the
> loader, but I don't think that should matter).  I see that the subject
> ID that it is complaining of not existing is fairly low: is there
> another GFF file that you loaded first?  I'm wondering if there is
> some bad interaction between them (there shouldn't be, so that would
> consitute a bug).  If there is one other GFF file, can you send that
> too?
>
> Thanks,
> Scott
>
>
> 2010/5/19 zhuangchao <[hidden email]>:
> > hello , Scott
> >
> > I   downloaded    Chado from svn . But  the question still  exist .
> >
> > The   gff file   is  in  the  attachment  . Here  is     a  history of
> >
> >  how I  loaded previous data  .   Thank  you very much !
> >
> > ===============================================
> > root@bnode6:/home/zc/Download#
> > perl /usr/local/bin/gmod_bulk_load_gff3.pl  --gfffile     NC_001437.gff
> > --organism 'Japanese encephalitis virus' --dbname four_viruses  --dbuser
> > zc --dbpass 123456 --dbhost localhost --dbport 5432  --save_tmpfiles
> >
> >
> > Preparing data for inserting into the four_viruses database
> > (This may take a while ...)
> > Dropping cds temp tables...
> > Creating cds temp tables...
> > NOTICE:  CREATE TABLE will create implicit sequence
> > "tmp_cds_handler_cds_row_id_seq" for serial column
> > "tmp_cds_handler.cds_row_id"
> > NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> > "tmp_cds_handler_pkey" for table "tmp_cds_handler"
> > NOTICE:  CREATE TABLE will create implicit sequence
> > "tmp_cds_handler_relationship_rel_row_id_seq" for serial column
> > "tmp_cds_handler_relationship.rel_row_id"
> > NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> > "tmp_cds_handler_relationship_pkey" for table
> > "tmp_cds_handler_relationship"
> >
> >
> > There are both CDS and exon features in this file, but
> > you did not set the --noexon option, which you probably want.
> > Please see `perldoc gmod_bulk_load_gff3.pl for more information.
> >
> > Loading data into feature table ...
> > Loading data into featureloc table ...
> > Loading data into feature_relationship table ...
> > Loading data into featureprop table ...
> > Skipping feature_cvterm table since the load file is empty...
> > Loading data into synonym table ...
> > Loading data into feature_synonym table ...
> > Loading data into dbxref table ...
> > Loading data into feature_dbxref table ...
> > Skipping analysisfeature table since the load file is empty...
> > Loading data into cvterm table ...
> > Loading data into db table ...
> > Skipping cv table since the load file is empty...
> > Skipping analysis table since the load file is empty...
> > Skipping organism table since the load file is empty...
> > DBD::Pg::db commit failed: ERROR:  insert or update on table
> > "feature_relationship" violates foreign key constraint
> > "feature_relationship_subject_id_fkey"
> > DETAIL:  Key (subject_id)=(66) is not present in table "feature".
> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh>
> > line 5.
> > commit failed: ERROR:  insert or update on table "feature_relationship"
> > violates foreign key constraint "feature_relationship_subject_id_fkey"
> > DETAIL:  Key (subject_id)=(66) is not present in table "feature".
> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3151, <$fh>
> > line 5.
> >
> > Abnormal termination, trying to clean up...
> >
> > Attempting to clean up the loader temp table (so that --recreate_cache
> > won't be needed)...
> > Trying to remove the run lock (so that --remove_lock won't be needed)...
> > Exiting...
> > =======================================================
> >
> >
> >
> > On Tue, 2010-05-18 at 09:07 -0400, Scott Cain wrote:
> >> Hi zhuangchao,
> >>
> >> Are you using Chado from the 1.0 release or from svn?  I believe that
> >> people have had that problem with the 1.0 release but it is fixed in
> >> svn.  You can get Chado from svn by following these directions and
> >> checking out the schema repository:
> >>
> >>   http://gmod.org/wiki/SVN
> >>
> >> (As a side note, I've promised myself to get the 1.1 release out this week.)
> >>
> >> If you are already using Chado from svn, please give us more
> >> information, like a sample of GFF that causes the problem, and perhaps
> >> a history of how you've loaded previous data (if you have).  Finally,
> >> you might want to use the option --save_tmpfiles and examine them for
> >> where in the GFF file the missing feature would have occurred that the
> >> database is complaining that it doesn't exist.
> >>
> >> Scott
> >>
> >>
> >> On Tue, May 18, 2010 at 2:54 AM, 庄超 <[hidden email]> wrote:
> >> > When I was loading the gff3 file into chado database using gmod_bulk_load_gff3.pl, I got  the errors like this:
> >> >
> >> > DBD::Pg::db commit failed: ERROR:  insert or update on table
> >> > "feature_relationship" violates foreign key constraint
> >> > "feature_relationship_subject_id_fkey"
> >> > DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
> >> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
> >> > line 41.
> >> >
> >> > commit failed: ERROR:  insert or update on table "feature_relationship"
> >> > violates foreign key constraint "feature_relationship_subject_id_fkey"
> >> > DETAIL:  Key (subject_id)=(31191) is not present in table "feature".
> >> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 2651, <$fh>
> >> > line 41.
> >> >
> >> > I don't know why and how to handle. Could you help me?
> >> > I am looking forward to your reply.  Thank you very much !
> >> >
> >> > --------------
> >> > zhuangchao
> >> > 2010-05-18
> >> >
> >> >
> >> >
> >> > ------------------------------------------------------------------------------
> >> >
> >> > _______________________________________________
> >> > Gmod-schema mailing list
> >> > [hidden email]
> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >> >
> >>
> >>
> >>
> >
>
>
>



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a question of loading the gff3 file into chado database (1)

zhuang chao
 hi , all :

 When I was loading the gff3 file into chado database using gmod_bulk_load_gff3.pl, I got  the errors like this:

 ==================================================
 Unable to find srcfeature MBU59461 in the database.
 ===================================================

 I don't know why and how to handle. Could you help me? I am looking  
 
 forward to your reply.  Thank you very much !


 Here  is   a  history  of how I  loaded  previous  data .

 =======================================================================

root@debian:/home/zc/Downloads#
perl /usr/local/bin/gmod_bulk_load_gff3.pl  --gfffile   sequences.gb.gff
--organism 'cdab' --dbname four_viruses  --dbuser zc --dbpass 123456
--dbhost localhost --dbport 5432  --recreate_cache  --noexon

(Re)creating the uniquename cache in the database...
Creating table...
Populating table...
Creating indexes...Done.
Preparing data for inserting into the four_viruses database
(This may take a while ...)


There is a CDS feature with no parent (ID:ODV-e28)  I think that is
wrong!


This GFF file has CDS and/or UTR features that do not belong to a
'central dogma' gene (ie, gene/transcript/CDS).  The features of
this type are being stored in the database as is.



There is a CDS feature with no parent (ID:ODV-e25)  I think that is
wrong!



There is a CDS feature with no parent (ID:helicase)  I think that is
wrong!

Dropping cds temp tables...
Creating cds temp tables...
NOTICE:  CREATE TABLE will create implicit sequence
"tmp_cds_handler_cds_row_id_seq" for serial column
"tmp_cds_handler.cds_row_id"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"tmp_cds_handler_pkey" for table "tmp_cds_handler"
NOTICE:  CREATE TABLE will create implicit sequence
"tmp_cds_handler_relationship_rel_row_id_seq" for serial column
"tmp_cds_handler_relationship.rel_row_id"
NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
"tmp_cds_handler_relationship_pkey" for table
"tmp_cds_handler_relationship"


There is a CDS feature with no parent (ID:NP_613096.1)  I think that is
wrong!



There is a CDS feature with no parent (ID:NP_613119.1)  I think that is
wrong!



There is a CDS feature with no parent (ID:NP_613164.1)  I think that is
wrong!



There is a CDS feature with no parent (ID:NP_613178.1)  I think that is
wrong!



There is a CDS feature with no parent (ID:NP_613188.1)  I think that is
wrong!



There is a CDS feature with no parent (ID:NP_613194.1)  I think that is
wrong!



There is a CDS feature with no parent (ID:NP_613231.1)  I think that is
wrong!



There is a CDS feature with no parent (ID:39k/pp31)  I think that is
wrong!



There is a CDS feature with no parent (ID:NP_613234.1)  I think that is
wrong!

Unable to find srcfeature MBU59461 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache'
option. at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4026

Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x34d6e30)', 'Bio::SeqFeature::Annotated=HASH(0x2cea988)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 758
Issuing rollback() due to DESTROY without explicit disconnect() of
DBD::Pg::db handle dbname=four_viruses;port=5432;host=localhost
at /usr/share/perl/5.10/Carp.pm line 45.
===================================================================================








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