gmod_bulk_load_gff3.pl error: DBD::Pg::db pg_endcopy failed

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gmod_bulk_load_gff3.pl error: DBD::Pg::db pg_endcopy failed

Collett, James R-2

Hello,

I'm trying to use gmod_bulk_load_gff3.pl to load a validated gff3 file from SGD into a new installation of Chado 1.2 on RHEL 6, but it keeps failing at this point with the following error:


Loading data into dbxref table ...
DBD::Pg::db pg_endcopy failed: ERROR:  invalid input syntax for integer: ""
CONTEXT:  COPY dbxref, line 19, column db_id: "" at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 3258, <$fh> line 8094.

Can you give me some leads to resolve this?  

Thanks,

Jim


__________________________________________________
James R. Collett, Ph.D.
Chemical and Biological Process Development Group
Pacific Northwest National Laboratory


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Re: gmod_bulk_load_gff3.pl error: DBD::Pg::db pg_endcopy failed

Scott Cain
Hi James,

Something is going wrong when the loader tries to look up a database when constructing the input for the dbxref table.  To debug the problem, try loading the same file again but include the --save_files argument, which will keep the temporary files from being disposed of when the loader quits.  Then you can look at the file for the dbxref table and look for the one that has an empty second column (which might be line 8094 of the temp file).  The second column is the db_id, which is what the error message is complaining about missing.  Hopefully, the contents of that line will point you in a direction that will provide more information; for example, you can search the GFF file for the accession that is causing the problem, and determine if the db_id that the loader is looking for should be already created or not.

Scott


On Thu, Nov 10, 2011 at 12:52 AM, Collett, James R <[hidden email]> wrote:

Hello,

I'm trying to use gmod_bulk_load_gff3.pl to load a validated gff3 file from SGD into a new installation of Chado 1.2 on RHEL 6, but it keeps failing at this point with the following error:


Loading data into dbxref table ...
DBD::Pg::db pg_endcopy failed: ERROR:  invalid input syntax for integer: ""
CONTEXT:  COPY dbxref, line 19, column db_id: "" at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 3258, <$fh> line 8094.

Can you give me some leads to resolve this?

Thanks,

Jim


__________________________________________________
James R. Collett, Ph.D.
Chemical and Biological Process Development Group
Pacific Northwest National Laboratory


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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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Re: gmod_bulk_load_gff3.pl error: DBD::Pg::db pg_endcopy failed

Collett, James R-2

Hi Scott,

 

 

Line 8094 appears at the very end of my  chado-feature_dbxref-v6IO.dat file.  There’s no characters on it, as shown below with the formatting highlighted.  Is this normal?

 

   8090 96585^I12^IS000007218^I1^I\N$

   8091 96586^I12^IS000007219^I1^I\N$

   8092 96587^I12^IS000007220^I1^I\N$

   8093 \.$

   8094 $

 

Thanks,

 

Jim

From: Scott Cain [mailto:[hidden email]]
Sent: Thursday, November 10, 2011 7:06 AM
To: Collett, James R
Cc: [hidden email]
Subject: Re: [Gmod-schema] gmod_bulk_load_gff3.pl error: DBD::Pg::db pg_endcopy failed

 

Hi James,

Something is going wrong when the loader tries to look up a database when constructing the input for the dbxref table.  To debug the problem, try loading the same file again but include the --save_files argument, which will keep the temporary files from being disposed of when the loader quits.  Then you can look at the file for the dbxref table and look for the one that has an empty second column (which might be line 8094 of the temp file).  The second column is the db_id, which is what the error message is complaining about missing.  Hopefully, the contents of that line will point you in a direction that will provide more information; for example, you can search the GFF file for the accession that is causing the problem, and determine if the db_id that the loader is looking for should be already created or not.

Scott

On Thu, Nov 10, 2011 at 12:52 AM, Collett, James R <[hidden email]> wrote:


Hello,

I'm trying to use gmod_bulk_load_gff3.pl to load a validated gff3 file from SGD into a new installation of Chado 1.2 on RHEL 6, but it keeps failing at this point with the following error:


Loading data into dbxref table ...
DBD::Pg::db pg_endcopy failed: ERROR:  invalid input syntax for integer: ""
CONTEXT:  COPY dbxref, line 19, column db_id: "" at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 3258, <$fh> line 8094.

Can you give me some leads to resolve this?

Thanks,

Jim


__________________________________________________
James R. Collett, Ph.D.
Chemical and Biological Process Development Group
Pacific Northwest National Laboratory


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Register now
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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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