bulk_load_gff3.PLS: command not found

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/share/gmod/chado/load/bin/bulk_load_gff3.PLS - from package: libchado-perl

You may install the required package with command apt-get install {package}

Error in other languages:
bulk_load_gff3.PLS: bevel nie gevind nie
bulk_load_gff3.PLS: comandă negăsită
bulk_load_gff3.PLS: comando não encontrado
bulk_load_gff3.PLS: commande introuvable
bulk_load_gff3.PLS: command not found
bulk_load_gff3.PLS: käsku ei ole
bulk_load_gff3.PLS: không tìm thấy lệnh
bulk_load_gff3.PLS: komanda nerasta
bulk_load_gff3.PLS: Kommando nicht gefunden.
bulk_load_gff3.PLS: kommandot finns inte
bulk_load_gff3.PLS: komut yok
bulk_load_gff3.PLS: nie znaleziono polecenia
bulk_load_gff3.PLS: níor aimsíodh an t-ordú
bulk_load_gff3.PLS: no se encontró la orden
bulk_load_gff3.PLS: no s'ha trobat l'ordre
bulk_load_gff3.PLS: opdracht niet gevonden
bulk_load_gff3.PLS: parancs nem található
bulk_load_gff3.PLS: perintah tidak ditemukan
bulk_load_gff3.PLS: príkaz nenájdený
bulk_load_gff3.PLS: příkaz nenalezen
bulk_load_gff3.PLS: команда не найдена
bulk_load_gff3.PLS: командата не е открита
bulk_load_gff3.PLS: 命令找不到
bulk_load_gff3.PLS: コマンドが見つかりません