indexpub: 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/indexpub - from package: ncbi-tools-bin

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

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