A thought on this is that the command line flash requires sudo. You didn’t mention that, but if not, then that might be the cause.
If you did use sudo, then the command would first generate “Linux_for_Tegra/bootloader/system.img.raw”, and then generate the sparse “bootloader/system.img” from that. This is a lot of file space, and if your system does not have enough space, perhaps it stopped. From the “Linux_for_Tegra/” directory, what do you see from “df -H -T .” (the “.” is important…you could instead name the full path to the “Linux_for_Tegra/” location).
Also, if you go to “Linux_for_Tegra/bootloader/”, what do you see from “ls -lh system.img*”?