fastq_masker: 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
/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/fastq_masker - from package: fastx-toolkit

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