Doing some video editing on linux, I wanted to convert the videos to a format easy to edit (and deinterlaced). I found this blog post: http://www.itc4u.net/it-chalk-board/67-linux-app-ffmpeg/115-edit-avchd-files-mts-with-blender-or-cinelerraconvert-mts-to-dnxhd-mov.html
Which seemed great, except when I ran the command he gave, I got the error "Could not write header for output file #0". (Stream 0 being the video stream). A bit cryptic. I eventually managed to figure out that this is due to the container format. Specifically, I was trying to encode it into an AVI. Apparently the Dnxhd encoder doesn't like this. If you encode it to a .mov, it works perfectly.