Robot Unable to track path - (tf2 empty frame id warning)

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I am currently running a differential drive setup robot configured to run on GMapping, custom made odometry publisher and navigation stack(move_base, costmap_2d). I have the following errors and warnings with the param settings given below:

1. I get the following error when giving a goal on the map (map and current position are perfect ).( I created a map from recording /scan topic on a bag file)

   [ WARN] [1487352631.099260113]: MessageFilter [target=map ]: Discarding message from [/move_base] due to empty frame_id. This message will only print once.

   [ WARN] [1487352631.099750851]: Invalid argument passed to canTransform argument source_frame in tf2 frame_ids cannot be empty

2. move_base linear and angular velocities aren't getting tracked. The robot just weirdly rotates at full speed and performs in place rotation, and goes away from the goal given. BUT , using keyboard to publish cmd_vel works and the robot moves around perfectly. Which suggests the move_base isn't configured properly.

3. Sometimes, the above two problems don't come up but the robot veers away just as it reaches the goal at a high speed(away from the goal).

The robot has a square base with motors kept at either centres of sides of square with a castor wheel at center.

My setup files are:

  TrajectoryPlannerROS:
      acc_lim_x: 0.09
      acc_lim_y: 0.0
      acc_lim_theta: .05
      max_vel_x: 0.6
      min_vel_x: 0.3
      max_vel_theta: 0.2
      min_vel_theta: 0.1
      min_in_place_vel_theta: 0.2
      holonomic_robot: false
      yaw_goal_tolerance: .2
      xy_goal_tolerance: .2
      sim_time: 1.0
      vx_samples: 12
      meter_scoring: true
      pdist_scale: 15
      heading_lookahead: 0.325
      heading_scoring: true
      dwa: true
      global_frame_id: map



     global_costmap:
          global_frame: /map
          robot_base_frame: /base_link
          update_frequency: 1.0 #before: 5.0
          publish_frequency: 0.5 #before 0.5
          static_map: true
          transform_tolerance: 0.5

    local_costmap:
      global_frame: /map
      robot_base_frame: /base_link
      update_frequency: 1.0 #before 5.0
      publish_frequency: 2.0 #before 2.0
      static_map: false
      rolling_window: true
      width: 5
      height: 5
      resolution: 0.025 #before 0.05
      transform_tolerance: 0.5

common_costmap:
    obstacle_range: 2.5
    raytrace_range: 3.0
    footprint: [[0.15, 0.15], [-0.15, 0.15], [-0.15, -0.15], [0.15, -0.15]]
    inflation_radius: 0.15
    transform_tolerance: 0.13
    meter_scoring: true
    observation_sources: scan
    scan:
      data_type: LaserScan
      topic: scan
      marking: true
      clearing: true
    map_type: costmap

move_base_params
    shutdown_costmaps: false
    controller_frequency: 5.0 #before 5.0
    controller_patience: 15
    planner_frequency: 5.0
    planner_patience: 5.0
    oscillation_timeout: 10.0
    oscillation_distance: 0.2
    conservative_reset_dist: 0.10 #distance from an obstacle at which it will unstuck itself
    recovery_behavior_enabled: false
    clearing_rotation_allowed: false