fastq_quality_filter: 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/fastq_quality_filter - from package: fastx-toolkit

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

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