fasta_clipping_histogram.pl: 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_clipping_histogram.pl - from package: fastx-toolkit

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

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