htseq-qa: 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/htseq-qa - from package: python-htseq

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

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