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First parse the files with ffmpeg and set all at the same resolution & size, then use ffmpeg to create the mp4. A simple script to process the files one at a time would handle that with only the delay needed for the sizing.
It can be done in a single pass but is much easier if you do one thing at a time and not jumping back and forth between tasks.
If the jpeg's are different size, then find the largest one and make the video that size, pad the rest of the jpegs to that size. Or pad all of them to a size larger than the largest jpeg.
Example where largest jpeg is 1000x600. Pad all the rest to that size. Images show for 5 seconds, 30 fps x264 mp4.
^ well don't use .mpeg then.
Nobody suggested it, either.
Use .mp4, .mkv
(the name "ffmpeg" is somewhat historical at this point)
It looks like you aren't actually using the examples you're given?
I'm still a bit unsure what you're trying to achive there (some sort of slideshow as a movie, I guess), but generally speaking:
keep in mind that in ffmpeg it matters where you put command line options - before the input file, or before the output file.
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