On Fri, Jul 18, 2014 at 10:33:40PM +0100, JULIAN GARDNER wrote:
[...]
> fmpeg -i xxxx.ts -vcodec libx264 -b:v 1000k -acodec libfaac -async 1 -vf 
> 'split [mark], drawbox=10:10:100:100:color=green [dontneed];[mark] 
> drawbox=100:100:100;100:color=red [vid];[dontneed][vid] overlay' -y -f mpegts 
> processed.ts
> 

try -filter_complex instead of -vf and
-map [vid] -y -f mpegts processed.ts -map '[dontneed]' -f null -

[...]

-- 
Clément B.

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