fastaFromBed: 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 CentOS possible default full paths are:

/usr/bin/fastaFromBed - from package: BEDTools

You may install the required package with command yum install {package}

On Debian possible default full paths are:

/usr/bin/fastaFromBed - from package: BEDTools

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

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