It looks like your Apalis iMX6 target is not recognised on the Linux workstation side. Could you make sure you are using either X50 (USB-B recommended) or X49 (micro-USB 2.0, micro-USB 3.0 not supported/recommended) and definitely not both together. Then on the workstation side try listing them targets as follows:
[user@host ~]$ lsusb | grep -i free
Bus 001 Device 016: ID 15a2:0054 Freescale Semiconductor, Inc. i.MX 6Dual/6Quad SystemOnChip in RecoveryMode
If that works out OK try executing the recovery script again e.g. as follows:
[user@host Apalis-iMX6_ToradexEasyInstaller_1.1-20170906]$ ./recovery-linux.sh
Downloading Toradex Easy Installer...
[sudo] password for user:
Successfully downloaded Toradex Easy Installer.