Incorrect tiles from a shapefile are generated by mapnik

I used mapnik_node_tile_server to generate tiles from a shapefile created by gdal_contour.
The tile generation function is:

function fetchTile(layer, z, x, y, callback) {
  var map = new mapnik.Map(TILE_SIZE, TILE_SIZE); // TILE_SIZE = 256
  var layerPath = util.format('%s/layers/%s.xml', __dirname, layer);
  var tileFilePath = util.format('%s/tiles/%s/%d/%d/%d.png', __dirname, layer, z, x, y)
  var cachedTile = getCachedTile(tileFilePath);
  if (cachedTile) {
    callback(cachedTile);
  } else {
    var filePath = util.format('%s/tiles/%s/%d/%d/', __dirname, layer, z, x);
    mkdirp.sync(filePath);
    map.loadSync(layerPath);
    map.zoomToBox(mercator.bbox(x, y, z, false, '900913'));
    var im = new mapnik.Image(TILE_SIZE, TILE_SIZE);
    map.render(im, function(err, im) {
      if (err) console.log('error', err);
      file = im.saveSync(tileFilePath, 'png');
      callback(fs.readFileSync(tileFilePath));
    });
  }

}

Most of the contour lines are not rendered in the tiles and transparent areas are not created correctly.
Here is the shapefile drawn in QGIS and generated tiles in CesiumJS respectively.