You should enqueue scripts in functions.php itself with wp_enqueue_scripts hook. Like this.
function my_jsfile() {
wp_register_script( 'menu', get_template_directory_uri() . '/js/menu-effect.js', array() );
wp_register_script( 'thumbnail', get_template_directory_uri() . '/js/thumbnail-effect.js', array() );
wp_enqueue_script( 'menu' );
wp_enqueue_script( 'thumbnail' );
}
add_action( 'wp_enqueue_scripts', 'my_jsfile' );
And also you should remove wp_enqueue_script from header.php as well as script links.
And finally make sure your script paths are correct.
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