I love Linux, not only because it makes sense, but because the programs available for ham radio are in many cases superior to the Windows equivalents.  CQRLOG is one of them, and fldigi is another one that workwell with my small laptop and Elecraft KX3.  It took me a while to get them both working right, and here's a couple of tips so that others may not have to reinvent the wheel.
When you set up the CQRLOG TRX Control parameters, enter your rig name under "Radio one, desc:," use Rig ID model 229 (which is the one for the K3, but it works), click the "run rigctld when program starts" box, and specify only the serial speed of 4800 and 2 stop bits.  Leave the rest default.
It still won't work because when you plug the serial port adapter into your Linux machine, it will most likely recognize it but will prevent you from accessing it because you don't have permission to do so.  That's because you most likely don't belong to the proper group.  Part of Linux security.  
Here's a step by step guide to making it work permanently.
1.  Plug in your USB to serial port adapter and get your rig running
2.  Open a terminal window in Linux by pressing CTL-ALT-T.  You'll get a prompt which consists of your username, the computer you are running on and a dollar sign.  Mine is "steve@steve-Latitude-D420:~$"  From this prompt, enter the following commands.  Case is important.
3.  Discover what the USB adapter is called by entering:
 
ls /sys/class/tty
 
You'll get a list of perhaps 50 various devices; the last one is your adapter, and should be ttyUSB0 or ttyUSB1.  If you don't see it, you are in trouble and may have to install the proper drivers.  I didn't have that issue, but if you do, remember that Google Is Your Friend.
 
4.  Find out which user groups are authorized to access the adapter by entering:
 
ls -l /dev/ttyUSB0      (or ttyUSB1 if that's where your device ended up)
 
The output will show you what permissions have been granted, and to which user groups.  Mine shows that members of two groups can access it: root and dialout.  You don't want to become a member of the "root" group because that would compromise security.
 
5.  Find out which groups you belong to by entering:
 
groups
 
You'll probably see a long list of groups, but "dialout" isn't one of them.
 
6.  Join the dialout usergroup by entering:
 
sudo usermod -a -G dialout yourusername
 
7.  Reboot.
 
Hope it works for you.
 
73's
Steve