GFF Bulk Uploader error(s)

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GFF Bulk Uploader error(s)

Shane McCoy

Also, concerning this error: 

>>WARNING:
>>Unable to find a 'part_of' term in the relationship ontology;
>>It's absense indicates that there is something really wrong with the
>>database.
>>Consider stopping and checking the state of your cvterm table.

This is my sql query results:

sbass_ncsu=> Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of'; 


 cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete | is_relationshiptype |     name     

-----------+-------+---------+------------+-----------+-------------+---------------------+--------------

        37 |     7 | part_of |            |        39 |           0 |                   1 | relationship

        95 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)



Date: Mon, 8 Dec 2014 21:30:46 -0500
From: Shane McCoy <[hidden email]>
Subject: [Gmod-schema] GFF Bulk Uploader error(s)
To: [hidden email]
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

 Hello! Tried uploading multiple GFF files tonight and got these errors.
I did read on GMOD mailing list archives about 'Warning' part_of issue here:
http://generic-model-organism-system-database.450254.n5.nabble.com/Unable-to-find-a-part-of-term-in-the-relationship-ontology-td5712524.html
though i'm not sure still what to do. (the schema is set in 'public' fyi)
Thanks for looking!
Shane M.


gmod_bulk_load_gff3.pl --noexon --analysis --organism striped bass
--gfffile SBDraft_Pt1.all.gff SBDraft_Pt2.all.gff SBDraft_Pt3.all.gff
SBDraft_Pt4.all.gff SBDraft_Pt5.all.gff

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 498.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 1078.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 1111.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 1144.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 1469.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 1664.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 1696.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 1728.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 1760.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 1977.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2007.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2037.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2067.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2099.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2284.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2313.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2345.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2376.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2409.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2443.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2474.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 2504.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 4872.

(Maybe you should just omit the defined()?)

WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the
database.
Consider stopping and checking the state of your cvterm table.

(Re)creating the uniquename cache in the database...
Creating table...
Populating table...
Creating indexes...
Adjusting the primary key sequences (if necessary)...Done.
Creating gff_meta table...
Preparing data for inserting into the sbass_ncsu database
(This may take a while ...)

DBD::Pg::st fetchrow_array failed: no statement executing at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm
line 1209, <GEN0> line 2.

striped organism not found in the database at
/home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl
line 749, <GEN0> line 2.

Abnormal termination, trying to clean up...
Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting...
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