bowtie-buildc: 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-buildc - from package: bowtie

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

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