bam2fastx: 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
/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/bam2fastx - from package: tophat

You may install the required package with command apt-get install {package}
Error in other languages:
bam2fastx: bevel nie gevind nie
bam2fastx: comandă negăsită
bam2fastx: comando não encontrado
bam2fastx: commande introuvable
bam2fastx: command not found
bam2fastx: käsku ei ole
bam2fastx: không tìm thấy lệnh
bam2fastx: komanda nerasta
bam2fastx: Kommando nicht gefunden.
bam2fastx: kommandot finns inte
bam2fastx: komut yok
bam2fastx: nie znaleziono polecenia
bam2fastx: níor aimsíodh an t-ordú
bam2fastx: no se encontró la orden
bam2fastx: no s'ha trobat l'ordre
bam2fastx: opdracht niet gevonden
bam2fastx: parancs nem található
bam2fastx: perintah tidak ditemukan
bam2fastx: príkaz nenájdený
bam2fastx: příkaz nenalezen
bam2fastx: команда не найдена
bam2fastx: командата не е открита
bam2fastx: 命令找不到
bam2fastx: コマンドが見つかりません