chado-fix-flybase-instance.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/chado-fix-flybase-instance.pl - from package: chado-utils

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

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