Real Robot and Rviz path is not matching

edit

Hi Good morning everyone!! I hope my question/query is not duplicated. If it is, I am really really sorry. I tried checking the answers similiar to my query but I couldn't find it. Any help would be highly appreciated.

I have a customized robot which I am trying to move it autonomously in my workshop. I am using amcl and move-base algorithm. The problem is when I am watching on rviz, its perfectly moving and planning path. But my customized robot is not even moving more than few centimeters.
I am using:

(1) ROS Kinetic (2) Ubuntu 16.04 LTS on Jetson TX2 (3) RP Lidar A1 (4) Arduino UNO for sending motor command via STM32F0-Discorvery board (CAN bus) to RoboteQ motor controller.

I am getting this warning messages

[ WARN] [1520556177.779801584]: Map update loop missed its desired rate of 5.0000Hz... the loop actually took 0.5349 seconds
[ WARN] [1520556178.214556518]: Control loop missed its desired rate of 5.0000Hz... the loop actually took 0.5679 seconds

This is my cmd_vel plot:

https://www.dropbox.com/s/x67lhcx2qf9...

Here are my launch files and configuration files:

(1) navigate.launch

<?xml version="1.0"?>
<launch>

    <master auto="start"/>
    <!-- Run my_robot compatible laser drivers -->
    <include file="$(find autonomous_driving)/launch/laser.launch" />

    <!-- Map server -->
    <arg name="map_file" default="$(find autonomous_driving)/maps/my_workshop.yaml"/>
    <node pkg="map_server" name="map_server"  type="map_server" args="$(arg map_file)" />

    <!-- AMCL used for localization -->
    <include file="$(find autonomous_driving)/launch/amcl.launch" />

    <!-- Calls navigation stack packages for compatible my_robot base -->

    <include file="$(find autonomous_driving)/launch/move_base/move_base.launch" />

    <node name="rviz" pkg="rviz" type="rviz" args="-d $(find autonomous_driving)/rviz/navigation.rviz"/>
</launch>

2) amcl.launch

<?xml version="1.0"?>
<launch>
<node pkg="amcl" type="amcl" name="amcl" output="screen">

  <remap from="scan" to="scan" />
  <remap from="cmd_vel" to="cmd_vel" />

  <remap from="scan" to="/scan" />

  <!-- Publish scans from best pose at a max of 10 Hz -->
  <param name="odom_model_type" value="diff"/>
  <param name="odom_alpha5" value="0.1"/>
  <param name="transform_tolerance" value="0.2" />
  <param name="gui_publish_rate" value="10.0"/>
  <param name="laser_max_beams" value="30"/>
  <param name="min_particles" value="500"/>
  <param name="max_particles" value="5000"/>
  <param name="kld_err" value="0.05"/>
  <param name="kld_z" value="0.99"/>
  <param name="odom_alpha1" value="0.2"/>
  <param name="odom_alpha2" value="0.2"/>
  <!-- translation std dev, m -->
  <param name="odom_alpha3" value="0.8"/>
  <param name="odom_alpha4" value="0.2"/>
  <param name="laser_z_hit" value="0.5"/>
  <param name="laser_z_short" value="0.05"/>
  <param name="laser_z_max" value="0.05"/>
  <param name="laser_z_rand" value="0.5"/>
  <param name="laser_sigma_hit" value="0.2"/>
  <param name="laser_lambda_short" value="0.1"/>
  <param name="laser_lambda_short" value="0.1"/>
  <param name="laser_model_type" value="likelihood_field"/>
  <!-- <param name="laser_model_type" value="beam"/> -->
  <param name="laser_likelihood_max_dist" value="2.0"/>
  <param name="update_min_d" value="0.2"/>
  <param name="update_min_a" value="0.5"/>
  <param name="odom_frame_id" value="odom"/>
  <param name="base_frame_id" value="base_link"/>
  <param name="global_frame_id" value="map"/>
  <param name="resample_interval" value="1"/>
  <param name="transform_tolerance" value="0.1"/>
  <param name="recovery_alpha_slow" value="0.0"/>
  <param name ...