Backstory: I have a system in place to automagically convert video files to 
smaller formats/versions on request to have a sort of "mobile version" for my 
father who travels extensively. The purpose is so that he can fit significantly 
more videos on his tablet than if they were the high quality rips.

It all boils down to:
ffmpeg -i [input-file] -ac 2 -c:v libx264 -c:a libmp3lame -b:v 1024k -preset 
fast [output-file]

I was under the impression everything was hunky dory until I took a bunch of 
the shrunken movies on my phone on a roadtrip. A good many of the videos were 
as good as can be expected, and nothing was egregiously wrong. However on a few 
videos the audio was absolutely atrocious, blown out, clipping, and just noise 
from seemingly nowhere. 

One of the worst was Intersteller which was completely unwatchable after the 
first two minutes with all the blown out crescendos, pops, cracks, static, and 
voices of the deep adulterating the audio stream. All video files affected by 
this were 5.1DTS sources, but not all 5.1DTS were affected.

When talking with my father he said it was a frequent enough occurrence that he 
suspected it was just because I had shrunk the file so small and was an 
artifact of that. He did confirm that most videos that were affected weren't as 
bad as the Interstellar conversion.


------------------------------------
~/testing$ ffmpeg -version
ffmpeg version 2.5.6-0ubuntu0.15.04.1 Copyright (c) 2000-2015 the FFmpeg 
developers
built with gcc 4.9.2 (Ubuntu 4.9.2-10ubuntu13)
configuration: --prefix=/usr --extra-version=0ubuntu0.15.04.1 
--build-suffix=-ffmpeg --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu 
--shlibdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu 
--enable-gpl --enable-shared --disable-stripping --enable-avresample 
--enable-avisynth --enable-ladspa --enable-libass --enable-libbluray 
--enable-libbs2b --enable-libcaca --enable-libcdio --enable-libflite 
--enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libgme 
--enable-libgsm --enable-libmodplug --enable-libmp3lame --enable-libopenjpeg 
--enable-libopus --enable-libpulse --enable-libschroedinger --enable-libshine 
--enable-libspeex --enable-libssh --enable-libtheora --enable-libtwolame 
--enable-libvorbis --enable-libwavpack --enable-libwebp --enable-libxvid 
--enable-opengl --enable-x11grab --enable-libdc1394 --enable-libiec61883 
--enable-libzvbi --enable-libzmq --enable-frei0r --enable-libvpx 
--enable-libx264 --enable-libsoxr --enable-gnut
 ls --enable-openal --enable-libopencv --enable-librtmp --enable-libx265
libavutil      54. 15.100 / 54. 15.100
libavcodec     56. 13.100 / 56. 13.100
libavformat    56. 15.102 / 56. 15.102
libavdevice    56.  3.100 / 56.  3.100
libavfilter     5.  2.103 /  5.  2.103
libavresample   2.  1.  0 /  2.  1.  0
libswscale      3.  1.101 /  3.  1.101
libswresample   1.  1.100 /  1.  1.100
libpostproc    53.  3.100 / 53.  3.100
------------------------------------

To troubleshoot I copied out a particularly bad snippet of audio
ffmpeg -i Int*.mkv -vn -c copy -ss 1:30 -t 0:30 inter.dts

This audio clip is confirmed to be a good 5.1dts stream


ffmpeg -i inter.dts -ac 2 -c libmp3lame inter-test.mp3
This audio sample has the exact same audio defects as in the shrunken video 

Converting it to a stereo wave format, and then converting into an mp3:
ffmpeg -i inter.dts -ac 2 -c pcm_s32le inter.wav && ffmpeg -i inter.wav -c 
libmp3lame inter.mp3
both inter.wav and inter.mp3 are confirmed to be GOOD stereo copies of the 
audio with no defects.

https://www.dropbox.com/s/tru46zo07gcr8ve/testing.tar.gz?dl=0
This is a link to the files in question to my testing above. 
inter.dts : 30 second rip of audio from video
inter-test : dts->mp3 conversion
inter.mp3 : dts->wav->mp3 conversion

I apologize if I'm missing something glaring, but I've been unable to find any 
other instances of this issue with my google-fu. Until I have a solution I've 
already edited my services to perform this intermediary wave step work-around 
on all conversions.

Thank you for your time.
                                          
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