Pouyan,
I think you were using the wrong lattice constant. The value of a should be for the unit cell, not the sublattice. Also, your basis vectors may not have been putting the correct atoms in place. The use of xmovie to view the output file is recommended to see if your lattice looks correct. You can assign each atom type a separate color. Try this in your script to build the lattice as I just tested it to make sure that it works with the latest LAMMPS version and the CdTe.sw potential file.
# bulk CdTe lattice
# CdTe Zincblende
# Define variable a set to CdTe SW lattice parameter
# Lattice parameter is set to 300K estimated value
variable a equal 6.54
# Pick units
units metal
atom_style atomic
boundary p p p
# Set up 8 atom zincblende unit cell,
lattice custom $a &
a1 1.0 0.0 0.0 &
a2 0.0 1.0 0.0 &
a3 0.0 0.0 1.0 &
basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 &
basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 &
basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 &
basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
# Set up 1 region
region reg1 block 0. 5. 0. 5. 0. 5.
# Create box with 1 region and 2 atom types
create_box 2 reg1
# Define zincblende basis atoms
create_atoms 1 region reg1 basis 5 2 basis 6 2 basis 7 2 basis 8 2
# Define atom properties and ID them
mass 1 112.41
mass 2 127.61
group Cd type 1
group Te type 2
# Set velocities to get starting temperature of 300K
velocity all create 600. 1452948
# Define force field
pair_style sw
pair_coeff * * CdTe.sw Cd Te
# Define the fix or time integration scheme
fix 1 all npt temp 300. 300. 10. aniso 0. 0. 10. drag 0.2
# Define output settings
dump mydump all custom 2000 dump.cdte.300.sw id type x y z
thermo_style custom step temp etotal ke pe press vol
thermo 200
timestep .001
restart 10000 cdte
# Compute
run 100000