Skip_tables.pm: command not found

Have You tried accessing the binary with the full path?

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/Skip_tables.pm - from package: chado-utils

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