look your AES.java:160

if (line.matches("[0-9A-F]+")) //If line is valid (i.e. contains valid hex characters, encrpyt. Otherwise, skip line.

Check file is matches

========= my tests =====
`java
public class WhyCannotAESFile {

public static void main(String[] args) {

    String[] params = {"e", "-length", "128", "-mode", "ecb", "/home/liuyy/Documents/debuglog/a.key", "/home/liuyy/Documents/debuglog/ss.log"};
    try {
        AES.main(params);
    } catch (IOException e) {
        e.printStackTrace();
    } finally {
    }

}

}

`

a.key

3c6e0b8a9c15224a8228b9a98ca1531d

ss.log
HelloWorld Test Dot