gmod_bulk_load_gff3.pl: 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/bin/gmod_bulk_load_gff3.pl - from package: chado-utils
/usr/share/gmod/chado/load/bin/gmod_bulk_load_gff3.pl - from package: libchado-perl

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

Error in other languages:
gmod_bulk_load_gff3.pl: bevel nie gevind nie
gmod_bulk_load_gff3.pl: comandă negăsită
gmod_bulk_load_gff3.pl: comando não encontrado
gmod_bulk_load_gff3.pl: commande introuvable
gmod_bulk_load_gff3.pl: command not found
gmod_bulk_load_gff3.pl: käsku ei ole
gmod_bulk_load_gff3.pl: không tìm thấy lệnh
gmod_bulk_load_gff3.pl: komanda nerasta
gmod_bulk_load_gff3.pl: Kommando nicht gefunden.
gmod_bulk_load_gff3.pl: kommandot finns inte
gmod_bulk_load_gff3.pl: komut yok
gmod_bulk_load_gff3.pl: nie znaleziono polecenia
gmod_bulk_load_gff3.pl: níor aimsíodh an t-ordú
gmod_bulk_load_gff3.pl: no se encontró la orden
gmod_bulk_load_gff3.pl: no s'ha trobat l'ordre
gmod_bulk_load_gff3.pl: opdracht niet gevonden
gmod_bulk_load_gff3.pl: parancs nem található
gmod_bulk_load_gff3.pl: perintah tidak ditemukan
gmod_bulk_load_gff3.pl: príkaz nenájdený
gmod_bulk_load_gff3.pl: příkaz nenalezen
gmod_bulk_load_gff3.pl: команда не найдена
gmod_bulk_load_gff3.pl: командата не е открита
gmod_bulk_load_gff3.pl: 命令找不到
gmod_bulk_load_gff3.pl: コマンドが見つかりません