you should split your command in Java into a String array and then pass it to getRuntime().exec(String[])
Short example:
String cmd[] = new String[]{
"ffmpeg",
"-r", String.valueOf(20/30f),
"-i", "assets/IMAG0054_BURST%03d.jpg",
"-i","assets/logo.png",
"-i","assets/guitar_tuning.wav","-r", "24", "-codec:a", "mp3",
"-filter_complex","[0:v][1:v]overlay=main_w-overlay_w-10:main_h-overlay_h-10,"+
"drawtext=fontfile=assets/OpenSans-Regular.ttf:text=1st scene:x=0:y=0:fontsize=100:fontcolor=white:enable='between(t,0.5,2.5)'," +
"drawtext=enable='between(t,2.6,5.5)':fontfile=assets/OpenSans-Regular.ttf:text=2nd scene:x=0:y=0:fontsize=100:fontcolor=white," +
"drawtext=enable='between(t,5.6,8.8)':fontfile=assets/OpenSans-Regular.ttf:text=3rd scene:x=0:y=0:fontsize=100:fontcolor=white," +
"drawtext=enable='between(t,8.9,30)':fontfile=assets/OpenSans-Regular.ttf:text=4rd scene:x=0:y=0:fontsize=100:fontcolor=white" +
"[out]",
"-map", "[out]", "-map", "2:0",
"-acodec","mp3",
//"-shortest " +
"simple_lapse.mp4"};
Process ffmpeg = Runtime.getRuntime().exec(cmd);
Hope it helps