./run_nyx shows stem's debug output

[atagar]

Migrated from ticket 27517.

I did not find out why I see stem's debug output with ./run_nyx from a fresh clone:

nyx_fresh$ ./run_nyx -d nyx.log
TRACE:stem:Nyx 2.0.4-dev Debug Dump
Stem Version: 1.6.0
Python Version: 2.7.15
Platform: Linux (debian buster/sid )
--------------------------------------------------------------------------------
Nyx Configuration (/home/user/.nyx/config):
[file doesn't exist]
--------------------------------------------------------------------------------
Saving a debug log to nyx.log, please check it for sensitive information before sharing it.
NOTICE:stem:No nyxrc loaded, using defaults. You can customize nyx by placing a configuration file at /home/user/.nyx/config (see https://nyx.torproject.org/nyxrc.sample for its options).
TRACE:stem:config entry 'tor_chroot' not found, defaulting to ''
TRACE:stem:Sent to tor: PROTOCOLINFO 1
TRACE:stem:Received from tor:
250-PROTOCOLINFO 1
250-AUTH METHODS=COOKIE,SAFECOOKIE,HASHEDPASSWORD COOKIEFILE="/var/run/tor/control.authcookie"
250-VERSION Tor="0.3.5.0-alpha-dev"
250 OK
Tor controller password: