Sorry for the delay in reply.
I ran ffmpeg with ulimit -a but it comes back with unrecognized option 'a'
It does that with both PHP and terminal.

ffmpeg version 4.0.1-static https://johnvansickle.com/ffmpeg/  Copyright (c) 
2000-2018 the FFmpeg developers
  built with gcc 6.3.0 (Debian 6.3.0-18+deb9u1) 20170516
  configuration: --enable-gpl --enable-version3 --enable-static --disable-debug 
--disable-ffplay --disable-indev=sndio --disable-outdev=sndio --cc=gcc-6 
--enable-fontconfig --enable-frei0r --enable-gnutls --enable-gray 
--enable-libaom --enable-libfribidi --enable-libass --enable-libvmaf 
--enable-libfreetype --enable-libmp3lame --enable-libopencore-amrnb 
--enable-libopencore-amrwb --enable-libopenjpeg --enable-librubberband 
--enable-libsoxr --enable-libspeex --enable-libvorbis --enable-libopus 
--enable-libtheora --enable-libvidstab --enable-libvo-amrwbenc --enable-libvpx 
--enable-libwebp --enable-libx264 --enable-libx265 --enable-libxml2 
--enable-libxvid --enable-libzimg
  libavutil      56. 14.100 / 56. 14.100
  libavcodec     58. 18.100 / 58. 18.100
  libavformat    58. 12.100 / 58. 12.100
  libavdevice    58.  3.100 / 58.  3.100
  libavfilter     7. 16.100 /  7. 16.100
  libswscale      5.  1.100 /  5.  1.100
  libswresample   3.  1.100 /  3.  1.100
  libpostproc    55.  1.100 / 55.  1.100
Splitting the commandline.
Reading option 'ulimit' ... matched as output url.
Reading option '-a' ...Unrecognized option 'a'.
Error splitting the argument list: Option not found

________________________________
From: ffmpeg-user <[email protected]> on behalf of André Hänsel 
<[email protected]>
Sent: Tuesday, 26 June 2018 7:59 PM
To: 'FFmpeg user questions'
Subject: Re: [FFmpeg-user] ff_frame_thread_encoder_init failed when run via PHP 
exec

> > It works perfectly when I log in to the console via putty and run it. But
> > when I run it via exec() in PHP it always comes back with
> > ff_frame_thread_encoder_init failed Error initializing output stream 0:0 --
> > Error while opening encoder for output stream #0:0 - maybe incorrect
> > parameters such as bit_rate, rate, width or height.

Could you try running "ulimit -a", once on the console and once from PHP?

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