bowtie-build-l: 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/bowtie-build-l - from package: bowtie

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

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