fastaindex: 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/fastaindex - from package: exonerate

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

On Debian possible default full paths are:

/usr/bin/fastaindex - from package: exonerate

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

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