Need to acquire data from USB-1608GX over the course of 3 days at 50khz rate. What software should I use?

[blackpaper]

It does not seem like DAQami will work well for this use case. I am looking to log all the voltages to a file.

[DAQman]

I recommend the DASYLab software. 

https://www.mccdaq.com/products/dasylab.aspx

The LITE version will allow you to acquire, display and log the data to a file, and if you want, play it back. The Write Data module also has a multi-file feature. It can be set to index the file after a set amount of data. For instance, a file with the name myData would be turned into myData00, myData01, myData02, etc., each one picking up where the last left off.