FFmpeg render portrait oriented .mov files incorrectly

Question

When I try to convert a portrait oriented .mov file to mp4 file using the following commnad

ffmpeg -i "2.mov" -s 720x404 -ac 2 -threads 0 -c:v libx264 -pix_fmt yuv420p -vprofile high -level 4.1 -preset medium -crf 25 -maxrate:v 1000k -b:a 128k "r5.mp4"

the mp4 file that gets created looks stretched sideways like in this example. Can't paste the .mov or the .mp4 files but the problem is clear. What is the proper command to run to get a normal not stretched file?

the full log:

C:\ffmpeg> .\ffmpeg -i "1.mov" -s 720x404 -ac 2 -threads 0 -c:v libx264 -pix_fmt yuv420p -vprofile high -level 4.1 -preset medium -crf 25 -maxrate:v 1000k -b:a 128k "r7.mp4"
ffmpeg version N-79906-gc8c14d0 Copyright (c) 2000-2016 the FFmpeg developers
  built with gcc 5.3.0 (GCC)
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-avisynth --enable-bzlib --enable-fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype --enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-libmfx --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-libschroedinger --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-lzma --enable-decklink --enable-zlib
  libavutil      55. 24.100 / 55. 24.100
  libavcodec     57. 40.100 / 57. 40.100
  libavformat    57. 36.100 / 57. 36.100
  libavdevice    57.  0.101 / 57.  0.101
  libavfilter     6. 45.100 /  6. 45.100
  libswscale      4.  1.100 /  4.  1.100
  libswresample   2.  0.101 /  2.  0.101
  libpostproc    54.  0.100 / 54.  0.100
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '1.mov':
  Metadata:
    major_brand     : qt
    minor_version   : 0
    compatible_brands: qt
    creation_time   : 2019-12-30 14:54:06
    com.apple.quicktime.make: Apple
    com.apple.quicktime.model: iPhone XR
    com.apple.quicktime.software: 13.1.2
    com.apple.quicktime.creationdate: 2019-12-30T08:54:06-0600
  Duration: 00:00:09.11, start: 0.000000, bitrate: 15792 kb/s
    Stream #0:0(und): Video: h264 (High) (avc1 / 0x31637661), yuv420p(tv, bt709), 1920x1080, 15543 kb/s, 29.97 fps, 29.97 tbr, 600 tbn (default)
    Metadata:
      rotate          : 90
      creation_time   : 2019-12-30 14:54:06
      handler_name    : Core Media Data Handler
      encoder         : H.264
    Side data:
      displaymatrix: rotation of -90.00 degrees
    Stream #0:1(und): Audio: aac (LC) (mp4a / 0x6134706D), 44100 Hz, stereo, fltp, 195 kb/s (default)
    Metadata:
      creation_time   : 2019-12-30 14:54:06
      handler_name    : Core Media Data Handler
    Stream #0:2(und): Data: none (mebx / 0x7862656D), 20 kb/s (default)
    Metadata:
      creation_time   : 2019-12-30 14:54:06
      handler_name    : Core Media Data Handler
    Stream #0:3(und): Data: none (mebx / 0x7862656D), 0 kb/s (default)
    Metadata:
      creation_time   : 2019-12-30 14:54:06
      handler_name    : Core Media Data Handler
    Stream #0:4(und): Data: none (mebx / 0x7862656D), 23 kb/s (default)
    Metadata:
      creation_time   : 2019-12-30 14:54:06
      handler_name    : Core Media Data Handler
[libx264 @ 0569cc00] VBV maxrate specified, but no bufsize, ignored
[libx264 @ 0569cc00] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 0569cc00] profile High, level 4.1
[libx264 @ 0569cc00] 264 - core 148 r2694 3b70645 - H.264/MPEG-4 AVC codec - Copyleft 2003-2016 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookahead_threads=1 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=25.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[mp4 @ 055f0460] Using AVStream.codec to pass codec parameters to muxers is deprecated, use AVStream.codecpar instead.
    Last message repeated 1 times
Output #0, mp4, to 'r7.mp4':
  Metadata:
    major_brand     : qt
    minor_version   : 0
    compatible_brands: qt
    com.apple.quicktime.creationdate: 2019-12-30T08:54:06-0600
    com.apple.quicktime.make: Apple
    com.apple.quicktime.model: iPhone XR
    com.apple.quicktime.software: 13.1.2
    encoder         : Lavf57.36.100
    Stream #0:0(und): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 720x404, q=2-31, 29.97 fps, 30k tbn (default)
    Metadata:
      handler_name    : Core Media Data Handler
      creation_time   : 2019-12-30 14:54:06
      encoder         : Lavc57.40.100 libx264
    Side data:
      cpb: bitrate max/min/avg: 1000000/0/0 buffer size: 0 vbv_delay: -1
    Stream #0:1(und): Audio: aac (LC) ([64][0][0][0] / 0x0040), 44100 Hz, stereo, fltp, 128 kb/s (default)
    Metadata:
      creation_time   : 2019-12-30 14:54:06
      handler_name    : Core Media Data Handler
      encoder         : Lavc57.40.100 aac
Stream mapping:
  Stream #0:0 -> #0:0 (h264 (native) -> h264 (libx264))
  Stream #0:1 -> #0:1 (aac (native) -> aac (native))
Press [q] to stop, [?] for help
frame=  273 fps= 43 q=-1.0 Lsize=     973kB time=00:00:09.17 bitrate= 869.4kbits/s speed=1.45x
video:817kB audio:145kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 1.136555%
[libx264 @ 0569cc00] frame I:2     Avg QP:26.36  size: 19820
[libx264 @ 0569cc00] frame P:69    Avg QP:26.68  size:  7276
[libx264 @ 0569cc00] frame B:202   Avg QP:30.73  size:  1459
[libx264 @ 0569cc00] consecutive B-frames:  1.1%  0.7%  0.0% 98.2%
[libx264 @ 0569cc00] mb I  I16..4:  6.9% 60.8% 32.3%
[libx264 @ 0569cc00] mb P  I16..4:  1.5%  6.2%  2.2%  P16..4: 48.0% 20.5%  8.1%  0.0%  0.0%    skip:13.5%
[libx264 @ 0569cc00] mb B  I16..4:  0.1%  0.2%  0.1%  B16..8: 46.6%  4.8%  0.7%  direct: 0.9%  skip:46.6%  L0:40.1% L1:53.0% BI: 6.9%
[libx264 @ 0569cc00] 8x8 transform intra:62.7% inter:75.7%
[libx264 @ 0569cc00] coded y,uvDC,uvAC intra: 68.9% 61.3% 22.1% inter: 13.2% 11.1% 0.7%
[libx264 @ 0569cc00] i16 v,h,dc,p:  6% 52%  6% 36%
[libx264 @ 0569cc00] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 11% 33% 13%  4%  6%  3% 15%  4% 12%
[libx264 @ 0569cc00] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 17% 38% 12%  3%  5%  3% 12%  2%  8%
[libx264 @ 0569cc00] i8c dc,h,v,p: 48% 39%  9%  4%
[libx264 @ 0569cc00] Weighted P-Frames: Y:8.7% UV:7.2%
[libx264 @ 0569cc00] ref P L0: 57.7% 25.2% 12.1%  4.8%  0.2%
[libx264 @ 0569cc00] ref B L0: 94.9%  3.7%  1.4%
[libx264 @ 0569cc00] ref B L1: 97.6%  2.4%
[libx264 @ 0569cc00] kb/s:734.59
[aac @ 0569abc0] Qavg: 1236.647

Answer 1

Preserve aspect ratio with scale filter instead of -s:

ffmpeg -i input.mov -c:v libx264 -vf "scale=720:-2,format=yuv420p" -c:a copy -movflags +faststart output.mp4

Also, your ffmpeg is old: download a new version.