bam_merge: 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/bam_merge - from package: tophat

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