First, you shouldn't use the same files when running your tests than when running your application in production. Because the test files are accessible to everyone that has access to the repository, which is a security fail.
As said in the comments, the problem is that when running your tests, the working directory is these of the source code (in fact, go copy the whole bunch into a temp directory prior to running the tests), while when you run the program for real, the working directory is the one you are running the command from, hence the wrong relative path.
What I would advise is to use a configuration option to get a the file from which load your file (or a base directory to use with your paths). Either using an environment variable (I strongly encourage you to do that, see the 12factors manofesto for details), a configuration file, a command-line flag, etc.