gistfile1.txt

Inserting and updating terms...
DONE UPDATING existing terms! 
**modified name for TO:0000039 - 'yield component (obsolete TO:0000039)' 
 **modified name for TO:0000380 - 'planthopper (obsolete TO:0000380)' 
 **modified name for TO:0000186 - 'environmental stress related trait (obsolete TO:0000186)' 
 **modified name for TO:0000256 - 'genetic trait (obsolete TO:0000256)' 
 **modified name for TO:0000219 - 'stem morphology (obsolete TO:0000219)' 
 **modified name for TO:0000091 - 'leafhopper (obsolete TO:0000091)' 
 **modified name for TO:0000174 - 'maturity trait (obsolete TO:0000174)' 
 **modified name for TO:0000596 - 'plant volume (sensu Poaceae) (obsolete TO:0000596)' 
 **modified name for TO:0001036 - 'stem senescence (obsolete TO:0001036)' 
 **modified name for TO:0000393 - 'yield and yield component (obsolete TO:0000393)' 
 **modified name for TO:0000002 - 'epigenetic trait (obsolete TO:0000002)' 
 **modified name for TO:0000362 - 'rot disease (obsolete TO:0000362)' 
 **modified name for TO:0000272 - 'plant survivability (obsolete TO:0000272)' 
 **modified name for TO:0000239 - 'plant genetic trait unknown (obsolete TO:0000239)' 
 **modified name for TO:0000066 - 'spot disease (obsolete TO:0000066)' 
 **modified name for TO:0000302 - 'smut disease (obsolete TO:0000302)' 
 TERM 0002711 has name total water soluble content, which also exists for term id 77512 with accession 0020088

An error occured! Rolling back! DBIx::Class::Storage::DBI::_dbh_execute(): DBI Exception: DBD::Pg::st execute failed: ERROR:  duplicate key value violates unique constraint "cvterm_c1"
DETAIL:  Key (name, cv_id, is_obsolete)=(total water soluble content, 56, 0) already exists. [for Statement "INSERT INTO cvterm ( cv_id, dbxref_id, definition, is_obsolete, name) VALUES ( ?, ?, ?, ?, ? ) RETURNING cvterm_id" with ParamValues: 1='56', 2='211399', 3='The concentration of water soluble components in the plant as determined by refractive index.', 4='0', 5='total water soluble content'] at gmod_load_cvterms.pl line 546

output for loading trait.obo

this line:
" TERM 0002711 has name total water soluble content, which also exists for term id 77512 with accession 0020088"
tells you that TO:0002711 has exactly the same cvterm.name as cvterm_id 77512 (which is TO:0020088)

This is either an error in the TO obo file, or a problem with the logic of data loading in the script.

Can you check the file first to see if these 2 terms are not obsolete but still have the same name?