bed2gff3: 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/bin/bed2gff3 - from package: gbrowse

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

Error in other languages:
bed2gff3: bevel nie gevind nie
bed2gff3: comandă negăsită
bed2gff3: comando não encontrado
bed2gff3: commande introuvable
bed2gff3: command not found
bed2gff3: käsku ei ole
bed2gff3: không tìm thấy lệnh
bed2gff3: komanda nerasta
bed2gff3: Kommando nicht gefunden.
bed2gff3: kommandot finns inte
bed2gff3: komut yok
bed2gff3: nie znaleziono polecenia
bed2gff3: níor aimsíodh an t-ordú
bed2gff3: no se encontró la orden
bed2gff3: no s'ha trobat l'ordre
bed2gff3: opdracht niet gevonden
bed2gff3: parancs nem található
bed2gff3: perintah tidak ditemukan
bed2gff3: príkaz nenájdený
bed2gff3: příkaz nenalezen
bed2gff3: команда не найдена
bed2gff3: командата не е открита
bed2gff3: 命令找不到
bed2gff3: コマンドが見つかりません