htseq-count: 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-count - from package: python-htseq

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

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