$file = 'video_file';
$config['upload_path'] = './video_folder/';
$config['allowed_types'] = 'mov|mpeg|mp3|avi';
$config['max_size'] = '50000';
$config['max_width']   = '';
$config['max_height']   = '';

$this->upload->initialize($config);
$this->load->library('upload', $config);

if(!$this->upload->do_upload($file))
{
// If there is any error
$err_msgs .= 'Error in Uploading video '.$this->upload->display_errors().'<br />';
}
else
{
$data=array('upload_data' => $this->upload->data());
$video_path = $data['upload_data']['file_name'];
  $directory_path = $data['upload_data']['file_path'];
$directory_path_full      = $data['upload_data']['full_path'];
$file_name = $data['upload_data']['raw_name'];

// ffmpeg command to convert video

exec("ffmpeg -i ".$directory_path_full." ".$directory_path.$file_name.".flv");

// $file_name is same file name that is being uploaded but you can give your custom video name after converting So use something like myfile.flv.

/// In the end update video name in DB
$array = array(
'video' => $file_name.'.'.'flv',
);
$this->db->set($array);
$this->db->where('id',$id); // Table where you put video name
$query = $this->db->update('user_videos');
}