mysql> use magento;
mysql> select * from index_process;
+------------+------------------------------+-----------------+---------------------+---------------------+-----------+
| process_id | indexer_code                 | status          | started_at          | ended_at            | mode      |
+------------+------------------------------+-----------------+---------------------+---------------------+-----------+
|          1 | catalog_product_attribute    | pending         | 2014-05-05 20:11:54 | 2014-05-05 20:11:55 | real_time |
|          2 | catalog_product_price        | pending         | 2013-12-30 11:19:23 | 2013-12-30 11:19:23 | real_time |
|          3 | catalog_url                  | pending         | 2013-04-25 18:50:10 | 2013-04-25 18:50:10 | manual    | <----should be manual
|          4 | catalog_product_flat         | pending         | 2013-12-27 11:53:30 | 2013-12-27 11:53:31 | real_time |
|          5 | catalog_category_flat        | pending         | 2013-04-12 09:19:07 | 2013-04-12 09:19:07 | real_time |
|          6 | catalog_category_product     | pending         | 2013-12-23 14:44:15 | 2013-12-23 14:44:25 | real_time |
|          7 | catalogsearch_fulltext       | pending         | 2013-12-26 14:48:44 | 2013-12-26 14:48:46 | manual    | <----should be manual
|          8 | cataloginventory_stock       | pending         | 2014-05-05 20:11:05 | 2014-05-05 20:11:05 | real_time |
|          9 | tag_summary                  | pending         | 2014-05-05 20:11:54 | 2014-05-05 20:11:54 | real_time |
|         36 | url_redirect                 | require_reindex |                NULL |                NULL | real_time |
|         37 | catalog_url_category         | require_reindex |                NULL |                NULL | real_time |
|         38 | catalog_url_product          | require_reindex |                NULL |                NULL | real_time |
|         39 | catalog_category_product_cat | require_reindex |                NULL |                NULL | real_time |
|         40 | targetrule                   | require_reindex |                NULL |                NULL | real_time |
+------------+------------------------------+-----------------+---------------------+---------------------+-----------+
14 rows in set (0.00 sec)

To update the two databases to manual indexing you can use the following commands:

mysql> update index_process
    -> set mode="manual"
    -> where indexer_code="catalog_url";

mysql> update index_process
    -> set mode="manual"
    -> where indexer_code="catalogsearch_fulltext";

A re-index all cron should be running once a day. Any more times and this can start causing lock issues on your device:

crontab -u root -l

@daily /usr/bin/php /var/www/vhosts/local.deals/htdocs/shell/indexer.php reindexall

mysql> SELECT indexer_code, TIMESTAMPDIFF(SECOND, started_at, ended_at) as duration from index_process ORDER BY duration DESC;
+---------------------------+----------+
| indexer_code              | duration |
+---------------------------+----------+
| catalog_url               |       16 | <----in seconds
| catalog_product_attribute |        2 |
| catalog_category_product  |        2 |
| catalogsearch_fulltext    |        2 |
| catalog_product_price     |        1 |
| catalog_product_flat      |        0 |
| catalog_category_flat     |        0 |
| cataloginventory_stock    |        0 |
| tag_summary               |        0 |
+---------------------------+----------+
9 rows in set (0.00 sec)