fastaoverlap: 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 CentOS possible default full paths are:

/usr/bin/fastaoverlap - from package: exonerate

You may install the required package with command yum install {package}

On Debian possible default full paths are:

/usr/bin/fastaoverlap - from package: exonerate

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

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