$ ffmpeg -i 20140814_003236.mp4 -vf transpose=2 20140814_003236_fl.mp4
ffmpeg version 0.8.15-4:0.8.15-0ubuntu0.12.04.1, Copyright (c) 2000-2014 the Libav developers
  built on Aug 10 2014 18:16:51 with gcc 4.6.3
*** THIS PROGRAM IS DEPRECATED ***
This program is only provided for compatibility and will be removed in a future release. Please use avconv instead.

Seems stream 0 codec frame rate differs from container frame rate: 180000.00 (180000/1) -> 90000.00 (180000/2)
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '20140814_003236.mp4':
  Metadata:
    major_brand     : isom
    minor_version   : 0
    compatible_brands: isom3gp4
    creation_time   : 2014-08-13 22:32:39
  Duration: 00:00:02.51, start: 0.000000, bitrate: 11425 kb/s
    Stream #0.0(eng): Video: h264 (Baseline), yuv420p, 1280x720, 12114 kb/s, PAR 1:1 DAR 16:9, 29.83 fps, 90k tbr, 90k tbn, 180k tbc
    Metadata:
      creation_time   : 2014-08-13 22:32:39
    Stream #0.1(eng): Audio: aac, 48000 Hz, stereo, s16, 122 kb/s
    Metadata:
      creation_time   : 2014-08-13 22:32:39
[buffer @ 0x255ed00] w:1280 h:720 pixfmt:yuv420p
[transpose @ 0x255b280] w:1280 h:720 dir:2 -> w:720 h:1280 rotation:counterclockwise vflip:0
[mpeg4 @ 0x255dc60] removing common factors from framerate
[mpeg4 @ 0x255dc60] timebase 1/90000 not supported by MPEG 4 standard, the maximum admitted value for the timebase denominator is 65535
Output #0, mp4, to '20140814_003236_fl.mp4':
    Stream #0.0(eng): Video: mpeg4, yuv420p, 720x1280 [PAR 1:1 DAR 9:16], q=2-31, 200 kb/s, 90k tbn, 90k tbc
    Metadata:
      creation_time   : 2014-08-13 22:32:39
    Stream #0.1(eng): Audio: aac, 48000 Hz, stereo, s16, 200 kb/s
    Metadata:
      creation_time   : 2014-08-13 22:32:39
Stream mapping:
  Stream #0.0 -> #0.0
  Stream #0.1 -> #0.1
Error while opening encoder for output stream #0.0 - maybe incorrect parameters such as bit_rate, rate, width or height