mafft-homologs.rb: 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/lib/mafft/bin/mafft-homologs.rb - from package: mafft

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

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