First of all: If you feed x265 with Y4M (YUV4MPEG2) files, then it should be able to recognize the video properties (pixel format, resolution, FPS, etc) automatically, but for really "raw" YUV files you need to explicitly specify "--input-res" and "--input-csp" as well as "--fps" explicitly for things to work properly. In any case, x265 should process the input file all the way to the end – unless limited with "--frames", of course.
When you say
"x265 [...] only encode some frames", does it exit
gracefully after encoding those frames, or did it maybe exit
prematurely due to a
crash? In the latter case, input processing probably is
not the problem at all...
(Oh, and I don't think x265 can read anything directly, except for Y4M and "raw" YUV, so
no h.264 or h.265)