How to read until end of file (EOF) using BufferedReader in Java?

You are consuming a line at, which is discarded

while((str=input.readLine())!=null && str.length()!=0)

and reading a bigint at

BigInteger n = new BigInteger(input.readLine());

so try getting the bigint from string which is read as

BigInteger n = new BigInteger(str);

   Constructor used: BigInteger(String val)

Aslo change while((str=input.readLine())!=null && str.length()!=0) to

while((str=input.readLine())!=null)

see related post string to bigint

readLine()
Returns:
    A String containing the contents of the line, not including any line-termination characters, or null if the end of the stream has been reached 

see javadocs

With text files, maybe the EOF is -1 when using BufferReader.read(), char by char. I made a test with BufferReader.readLine()!=null and it worked properly.