bowtie2-align-l: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH

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/bowtie2-align-l - from package: bowtie2

You may install the required package with command apt-get install {package}
Error in other languages:
bowtie2-align-l: bevel nie gevind nie
bowtie2-align-l: comandă negăsită
bowtie2-align-l: comando não encontrado
bowtie2-align-l: commande introuvable
bowtie2-align-l: command not found
bowtie2-align-l: käsku ei ole
bowtie2-align-l: không tìm thấy lệnh
bowtie2-align-l: komanda nerasta
bowtie2-align-l: Kommando nicht gefunden.
bowtie2-align-l: kommandot finns inte
bowtie2-align-l: komut yok
bowtie2-align-l: nie znaleziono polecenia
bowtie2-align-l: níor aimsíodh an t-ordú
bowtie2-align-l: no se encontró la orden
bowtie2-align-l: no s'ha trobat l'ordre
bowtie2-align-l: opdracht niet gevonden
bowtie2-align-l: parancs nem található
bowtie2-align-l: perintah tidak ditemukan
bowtie2-align-l: príkaz nenájdený
bowtie2-align-l: příkaz nenalezen
bowtie2-align-l: команда не найдена
bowtie2-align-l: командата не е открита
bowtie2-align-l: 命令找不到
bowtie2-align-l: コマンドが見つかりません