DBD::Pg::db pg_endcopy failed: ERROR: invalid input syntax for integer: ""

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DBD::Pg::db pg_endcopy failed: ERROR: invalid input syntax for integer: ""

Moore, Gary

I’m having no luck loading some maker output into a clean chado 1.2 database using gmod_bulk_load_gff3.pl.  I applied the fix suggested in the Chado FAQ to no effect.   Before I go any further mucking about,  I’m hoping someone – Scott?  - can point me in the right direction as I don’t know if this is typically a data issue or ???.  Some relevant versions:

 

BioPerl 1.006901

Chado 1.2

Maker-2.10

 

Error output:

 

Loading data into feature_relationship table ...

DBD::Pg::db pg_endcopy failed: ERROR:  invalid input syntax for integer: ""

CONTEXT:  COPY feature_relationship, line 411, column type_id: "" at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 3258, <$fh> line 419.

 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: calling endcopy for feature_relationship failed:

STACK: Error::throw

STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472

STACK: Bio::GMOD::DB::Adapter::copy_from_stdin /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:3258

STACK: Bio::GMOD::DB::Adapter::load_data /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:3180

STACK: /usr/bin/gmod_bulk_load_gff3.pl:1072

 

Thanks

Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





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Re: DBD::Pg::db pg_endcopy failed: ERROR: invalid input syntax for integer: ""

Scott Cain
Hi Gary,

This can be caused by a few things, generally related to the Parent and Derives_from tags.

To track down the line that is causing the problem, you can try to do the load again, but this time add the "--save_files" argument to keep the loader from throwing a way the temp files it uses while it's parsing the GFF file.  Then you can look at the feature_relationship file, identify the feature_id of the offending feature (it should be in the second number in the line), and then go to one of the other temp files to help you sort out what the problematic GFF line is (for example, you could look in the featureprop temp file for the offending feature_id (again, the second number) to look for tags that would help you identify the lines, or featureloc to identify the coordinates).

You can also check the cvterm table for the derives_from and part_of terms and verify that they belong to the relationship ontology.  Some times loaders will "take" those terms and move them into other ontologies.

Scott


On Sat, Mar 30, 2013 at 8:43 AM, Moore, Gary <[hidden email]> wrote:

I’m having no luck loading some maker output into a clean chado 1.2 database using gmod_bulk_load_gff3.pl.  I applied the fix suggested in the Chado FAQ to no effect.   Before I go any further mucking about,  I’m hoping someone – Scott?  - can point me in the right direction as I don’t know if this is typically a data issue or ???.  Some relevant versions:

 

BioPerl 1.006901

Chado 1.2

Maker-2.10

 

Error output:

 

Loading data into feature_relationship table ...

DBD::Pg::db pg_endcopy failed: ERROR:  invalid input syntax for integer: ""

CONTEXT:  COPY feature_relationship, line 411, column type_id: "" at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 3258, <$fh> line 419.

 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: calling endcopy for feature_relationship failed:

STACK: Error::throw

STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472

STACK: Bio::GMOD::DB::Adapter::copy_from_stdin /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:3258

STACK: Bio::GMOD::DB::Adapter::load_data /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:3180

STACK: /usr/bin/gmod_bulk_load_gff3.pl:1072

 

Thanks

Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





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for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
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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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Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
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Re: DBD::Pg::db pg_endcopy failed: ERROR: invalid input syntax for integer: ""

Moore, Gary

Thanks, Scott.  I’ve also discovered that maker2chado seems to be a good way of avoiding these issues.

-Gary

 

From: Scott Cain [mailto:[hidden email]]
Sent: Sunday, March 31, 2013 11:17 PM
To: Moore, Gary
Cc: [hidden email]
Subject: Re: [Gmod-schema] DBD::Pg::db pg_endcopy failed: ERROR: invalid input syntax for integer: ""

 

Hi Gary,

This can be caused by a few things, generally related to the Parent and Derives_from tags.

To track down the line that is causing the problem, you can try to do the load again, but this time add the "--save_files" argument to keep the loader from throwing a way the temp files it uses while it's parsing the GFF file.  Then you can look at the feature_relationship file, identify the feature_id of the offending feature (it should be in the second number in the line), and then go to one of the other temp files to help you sort out what the problematic GFF line is (for example, you could look in the featureprop temp file for the offending feature_id (again, the second number) to look for tags that would help you identify the lines, or featureloc to identify the coordinates).

You can also check the cvterm table for the derives_from and part_of terms and verify that they belong to the relationship ontology.  Some times loaders will "take" those terms and move them into other ontologies.

Scott

On Sat, Mar 30, 2013 at 8:43 AM, Moore, Gary <[hidden email]> wrote:

I’m having no luck loading some maker output into a clean chado 1.2 database using gmod_bulk_load_gff3.pl.  I applied the fix suggested in the Chado FAQ to no effect.   Before I go any further mucking about,  I’m hoping someone – Scott?  - can point me in the right direction as I don’t know if this is typically a data issue or ???.  Some relevant versions:

 

BioPerl 1.006901

Chado 1.2

Maker-2.10

 

Error output:

 

Loading data into feature_relationship table ...

DBD::Pg::db pg_endcopy failed: ERROR:  invalid input syntax for integer: ""

CONTEXT:  COPY feature_relationship, line 411, column type_id: "" at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 3258, <$fh> line 419.

 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: calling endcopy for feature_relationship failed:

STACK: Error::throw

STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472

STACK: Bio::GMOD::DB::Adapter::copy_from_stdin /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:3258

STACK: Bio::GMOD::DB::Adapter::load_data /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:3180

STACK: /usr/bin/gmod_bulk_load_gff3.pl:1072

 

Thanks

Gary

 

Gary Moore, Technical Lead

LCA Digital Commons Project

National Agriculture Library/USDA/ARS

Beltsville MD

 





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.


------------------------------------------------------------------------------
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete
for recognition, cash, and the chance to get your game on Steam.
$5K grand prize plus 10 genre and skill prizes. Submit your demo
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
_______________________________________________
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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