TrimmomaticSE: 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/TrimmomaticSE - from package: trimmomatic

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

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