contig_to_chr_coords: 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/contig_to_chr_coords - from package: tophat

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

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