ffmpeg statement for Anaglyph of Red-Cyan Color
stereo3d is a video filter so it has to be specified via a filterchain or complex. Since you have two inputs, and stereo3d only converts a single input from one form of 3D arrangement to another, you'll have to combine the two image sequences first. For which, you can use the hstack filter, which will place the two sequences side-by-side.

So,

ffmpeg -i "left%06d.jpg" -i "right%06d.jpg" -filter_complex "hstack,stereo3d=sbsl:arcc" video_arcc.mp4


By default, image sequences are treated as 25 FPS and hence so will the output, in this case. If the framerate is different, say 24, then the beginning will be

ffmpeg -framerate 24 -i left%06d.jpg" -framerate 24 -i "right%06d.jpg