SELECT 
  SQL_CALC_FOUND_ROWS products.product_id, 
  descr1.product as product, 
  companies.company as company_name, 
  products.product_type, 
  products.parent_product_id, 
  products.variation_sku, 
  companies.discreet_shipping as company_discreet_shipping 
FROM 
  cscart_products as products 
  LEFT JOIN cscart_product_descriptions as descr1 ON descr1.product_id = products.product_id 
  AND descr1.lang_code = 'en' 
  LEFT JOIN cscart_product_prices as prices ON prices.product_id = products.product_id 
  AND prices.lower_limit = 1 
  LEFT JOIN cscart_companies AS companies ON companies.company_id = products.company_id 
  INNER JOIN cscart_products_categories as products_categories ON products_categories.product_id = products.product_id 
  INNER JOIN cscart_categories ON cscart_categories.category_id = products_categories.category_id 
  AND (
    cscart_categories.usergroup_ids = '' 
    OR FIND_IN_SET(
      0, cscart_categories.usergroup_ids
    ) 
    OR FIND_IN_SET(
      1, cscart_categories.usergroup_ids
    )
  ) 
  AND cscart_categories.status IN ('A', 'H') 
  AND cscart_categories.storefront_id IN (0, 1) 
  LEFT JOIN cscart_product_popularity as popularity ON popularity.product_id = products.product_id 
WHERE 
  1 
  AND cscart_categories.category_id IN (828, 1455) 
  AND products.product_id NOT IN (65239) 
  AND companies.status IN ('A') 
  AND products.amount > 0 
  AND products.status IN ('A') 
  AND (
    products.usergroup_ids = '' 
    OR FIND_IN_SET(0, products.usergroup_ids) 
    OR FIND_IN_SET(1, products.usergroup_ids)
  ) 
  AND products.status IN ('A') 
  AND prices.usergroup_id IN (0, 0, 1) 
  AND products.parent_product_id = 0 
GROUP BY 
  products.product_id 
ORDER BY 
  popularity.total desc, 
  products.product_id ASC 
LIMIT 
  0, 12

Query time 0.04973

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "34.95"
    },
    "ordering_operation": {
      "using_filesort": true,
      "grouping_operation": {
        "using_temporary_table": true,
        "using_filesort": false,
        "nested_loop": [
          {
            "table": {
              "table_name": "cscart_categories",
              "access_type": "range",
              "possible_keys": [
                "PRIMARY",
                "c_status",
                "p_category_id"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "category_id"
              ],
              "key_length": "3",
              "rows_examined_per_scan": 2,
              "rows_produced_per_join": 0,
              "filtered": "4.00",
              "index_condition": "(`chocoramo`.`cscart_categories`.`category_id` in (828,1455))",
              "cost_info": {
                "read_cost": "1.40",
                "eval_cost": "0.01",
                "prefix_cost": "1.41",
                "data_read_per_join": "275"
              },
              "used_columns": [
                "category_id",
                "storefront_id",
                "usergroup_ids",
                "status"
              ],
              "attached_condition": "(((`chocoramo`.`cscart_categories`.`usergroup_ids` = '') or (0 <> find_in_set(0,`chocoramo`.`cscart_categories`.`usergroup_ids`)) or (0 <> find_in_set(1,`chocoramo`.`cscart_categories`.`usergroup_ids`))) and (`chocoramo`.`cscart_categories`.`status` in ('A','H')) and (`chocoramo`.`cscart_categories`.`storefront_id` in (0,1)))"
            }
          },
          {
            "table": {
              "table_name": "products_categories",
              "access_type": "ref",
              "possible_keys": [
                "PRIMARY",
                "pt"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "category_id"
              ],
              "key_length": "3",
              "ref": [
                "chocoramo.cscart_categories.category_id"
              ],
              "rows_examined_per_scan": 839,
              "rows_produced_per_join": 67,
              "filtered": "100.00",
              "using_index": true,
              "cost_info": {
                "read_cost": "0.44",
                "eval_cost": "6.71",
                "prefix_cost": "8.56",
                "data_read_per_join": "1K"
              },
              "used_columns": [
                "product_id",
                "category_id"
              ],
              "attached_condition": "(`chocoramo`.`products_categories`.`product_id` <> 65239)"
            }
          },
          {
            "table": {
              "table_name": "products",
              "access_type": "eq_ref",
              "possible_keys": [
                "PRIMARY",
                "status",
                "idx_parent_product_id"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "product_id"
              ],
              "key_length": "3",
              "ref": [
                "chocoramo.products_categories.product_id"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 6,
              "filtered": "10.06",
              "cost_info": {
                "read_cost": "16.78",
                "eval_cost": "0.68",
                "prefix_cost": "32.05",
                "data_read_per_join": "36K"
              },
              "used_columns": [
                "product_id",
                "product_type",
                "status",
                "company_id",
                "amount",
                "usergroup_ids",
                "parent_product_id",
                "variation_sku"
              ],
              "attached_condition": "((`chocoramo`.`products`.`parent_product_id` = 0) and (`chocoramo`.`products`.`amount` > 0) and (`chocoramo`.`products`.`status` = 'A') and ((`chocoramo`.`products`.`usergroup_ids` = '') or (0 <> find_in_set(0,`chocoramo`.`products`.`usergroup_ids`)) or (0 <> find_in_set(1,`chocoramo`.`products`.`usergroup_ids`))))"
            }
          },
          {
            "table": {
              "table_name": "companies",
              "access_type": "eq_ref",
              "possible_keys": [
                "PRIMARY"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "company_id"
              ],
              "key_length": "4",
              "ref": [
                "chocoramo.products.company_id"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 0,
              "filtered": "10.00",
              "cost_info": {
                "read_cost": "1.69",
                "eval_cost": "0.07",
                "prefix_cost": "34.42",
                "data_read_per_join": "10K"
              },
              "used_columns": [
                "company_id",
                "status",
                "company",
                "discreet_shipping"
              ],
              "attached_condition": "(`chocoramo`.`companies`.`status` = 'A')"
            }
          },
          {
            "table": {
              "table_name": "prices",
              "access_type": "ref",
              "possible_keys": [
                "usergroup",
                "product_id",
                "lower_limit",
                "usergroup_id"
              ],
              "key": "product_id",
              "used_key_parts": [
                "product_id"
              ],
              "key_length": "3",
              "ref": [
                "chocoramo.products_categories.product_id"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 0,
              "filtered": "30.00",
              "cost_info": {
                "read_cost": "0.17",
                "eval_cost": "0.02",
                "prefix_cost": "34.65",
                "data_read_per_join": "4"
              },
              "used_columns": [
                "product_id",
                "lower_limit",
                "usergroup_id"
              ],
              "attached_condition": "((`chocoramo`.`prices`.`lower_limit` = 1) and (`chocoramo`.`prices`.`usergroup_id` in (0,0,1)))"
            }
          },
          {
            "table": {
              "table_name": "popularity",
              "access_type": "eq_ref",
              "possible_keys": [
                "PRIMARY",
                "total"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "product_id"
              ],
              "key_length": "3",
              "ref": [
                "chocoramo.products_categories.product_id"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 0,
              "filtered": "100.00",
              "cost_info": {
                "read_cost": "0.05",
                "eval_cost": "0.02",
                "prefix_cost": "34.72",
                "data_read_per_join": "6"
              },
              "used_columns": [
                "product_id",
                "total"
              ]
            }
          },
          {
            "table": {
              "table_name": "descr1",
              "access_type": "eq_ref",
              "possible_keys": [
                "PRIMARY",
                "product_id"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "product_id",
                "lang_code"
              ],
              "key_length": "9",
              "ref": [
                "chocoramo.products_categories.product_id",
                "const"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 0,
              "filtered": "100.00",
              "cost_info": {
                "read_cost": "0.20",
                "eval_cost": "0.02",
                "prefix_cost": "34.95",
                "data_read_per_join": "792"
              },
              "used_columns": [
                "product_id",
                "lang_code",
                "product"
              ]
            }
          }
        ]
      }
    }
  }
}