sra-pileup: 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/sra-pileup - from package: sra-toolkit

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