fasta_formatter: 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 Debian possible default full paths are:

/usr/bin/fasta_formatter - from package: fastx-toolkit

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

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