Can't find .env files during PHPUnit test using PUTTY

I'm using a vagrant box for my php project. I've created two .env files (.env and .env.testing). The website runs smoothly but while testing the functions using PHPUnit, it throws me a File Not found error. I can see the files on my directory but can't view them in terminal using ls. But I can see them all if I use ls -a command. Is the issue with vagrant or putty or am I doing this wrong?