flankBed: 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/flankBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/flankBed - from package: BEDTools

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

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