Regarding Convert MKV or AVI to MP4 with Render in - Ubuntu Linux CLI

I did the following to convert my video

First I

mkvextract tracks video.mkv 0:video.h264 1:audio.aac

Then I did this

MP4Box -split 800 video.mp4

All went well.

Question is as I got a subtitle in track 3, how do I render into my video.mp4 output as hard sub, what should I add in.

I used HandBrakeCLI & FFmpeg to convert the same video, it seems my convert code went wrong or so, when I try split with mp4box, it will stuck at 99%

But when I extract and merge it with mp4box, all went well, splitting etc. (without burning subtitle in)

This is my ffmpeg command line

ffmpeg -i "video.mkv" -acodec copy -vcodec libx264 -report -qscale 0 "video.mp4"
It just that after I convert finish with ffmpeg, I did a MP4Box -split 800 and the mp4box hang at 99%

below is my handbrakecli command line, no matter i use ffmpeg or handbrakecli, both give me a stuck at 99% splitting when using mp4box.

$command1 = '/usr/bin/HandBrakeCLI -i "'.$processing_folder. "/" . $file.'" -f mp4 -o "'.$newpath.'" -q '.$quality.' -e x264 --x264-preset medium --x264-tune animation --x264-profile high -x nr=1000 -m -E $