No Si (100) peak could be due to:

Film thickness. Film is too thick (unlikely)

Substrate is single crystal (epitaxial) but off optic axis

Dear Sir, Thanks for your comments !

Film thickness is around 160 nm.

What is meaning of off optic axis? could you please elaborate more?

When substrate is a single crystal a small deviation of the substrate perpendicular (in this case (100)) from normal axis will result in focused diffracted x-ray beam falls inside or outside the measurement/ focusing circle and no reflection will be detected by detector. This normally happens when substrate isn't placed in specimen holder properly. Try it again making sure substrate surface normal same as system set up normal. see file

Here is one way to actually discard the "blind-fold" of conventional diffractograms in all XRD labs in modern times. Besides, it is a lot more fun observing 2D XRD data in real time as the data is being collected. Aligning and optimizing reflections this way is safe, remote, quick, precise and dramatic  :-)

The famous NIST 2000 Standard Reference Material using the Bruker D8 and a sealed tube unit

maybe your silicon wafer is oxidised, with a coating of thick amorphous silicon dioxide coating on it, and you are unable to get any XRD reflections.

Just put a metal piece/sheet (aluminum or copper) or put any other material and see if your detector is working. If you are seeing peaks on other materials, then your system is working fine.

Take a normal silicon wafer, etch it buffered HF acid, and remove all oxide layers, and see if you detect the single crystal silicon peak. 

Dear Sreenivas Sir, thank you for your comments. I am using a substrate which is also thermally oxidized (SiO2) and assume thickness of SiO2 layer on the Si(100) substrate of the order of 100 nm. If I ignore that there is no peak from the substrate, I should get peak from the material. But I get only a small peak with intensity of 3.