Whoops left in a little debugging thing. The Command doesn't seem to get the errors from the stream maybe? But the setup file works fine from normal terminal exec.

main.go

@@ -59,7 +59,7 @@ func prep_query(db *sql.DB, q string) (*sql.Stmt){
 
 func main() {
 	// exec setup.sql to init
-  cmd := exec.Command("sqlite3", "rpgqui.db < sedfsftup.sql")
+  cmd := exec.Command("sqlite3", "rpgqui.db < setup.sql")
   out, err := cmd.Output()
 
   if err != nil {