blat2gff: 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/blat2gff - from package: gff2aplot

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

Error in other languages:
blat2gff: bevel nie gevind nie
blat2gff: comandă negăsită
blat2gff: comando não encontrado
blat2gff: commande introuvable
blat2gff: command not found
blat2gff: käsku ei ole
blat2gff: không tìm thấy lệnh
blat2gff: komanda nerasta
blat2gff: Kommando nicht gefunden.
blat2gff: kommandot finns inte
blat2gff: komut yok
blat2gff: nie znaleziono polecenia
blat2gff: níor aimsíodh an t-ordú
blat2gff: no se encontró la orden
blat2gff: no s'ha trobat l'ordre
blat2gff: opdracht niet gevonden
blat2gff: parancs nem található
blat2gff: perintah tidak ditemukan
blat2gff: príkaz nenájdený
blat2gff: příkaz nenalezen
blat2gff: команда не найдена
blat2gff: командата не е открита
blat2gff: 命令找不到
blat2gff: コマンドが見つかりません