How to remove the negative component of a sine wave?
The LM358 OpAmp you're using has an Input Bias Current spec (from table 6.5 on pg.5 of the DS) of typically 45nA.
If you refer to the internal schematic diagram in Fig.16 on pg.13:

you can see where this current comes from.
The current from the 6uA source is split between the 2 input legs and even though the majority of it will flow to ground through the input transistors, some of it still needs to flow out of the input pins in order to bias those transistors.  

When you use the opamp in a circuit, you must provide a path for this input bias current.  

In your circuit, all of the opamps inverting (-) inputs have a feedback resistor which does this job, and the first 3 have their non-inverting (+) inputs are either dc-coupled to each other or fed by a resistor voltage-divider.
But your 4th opamp is AC-coupled by C6 and has no DC path for the bias current being sourced by the non-inverting input.  

The easiest way to fix this in your circuit would be to put a resistor in parallel with D1.
To calculate the value of this resistor ou need to take the value of the bias current and decide for yourself what the maximum permissible offset voltage you can tolerate at that point is. Ohm's law will then produce a value for you.
You'll also need to be aware that this will form a high-pass filter with C6.