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Short question:

blender -b knob.blend -s 1 -e 2 -a -o //__targets/knob_#.png

Does not write to the desired files, but 0001.png, and 0002.png. I want the files __targets/knob_1.png and __targets/knob_2.png. It appears that blender ignores the target option in this case. What should I do to make it work?

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Blender executes the command line options in the over they are given, so Blender sees the command to render (-a) and then sets the command to set the output path (-o). This means the output path gets set after the render has happened.

You just need to swap the order of the commands so you have:

blender -b knob.blend -s 1 -e 2 -o //__targets/knob_#.png -a
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