What I can see in php error log is that during step [data: dbscripts/xml/upgrade/3.0.0_update.xml] it prints this:
[12-Dec-2016 10:38:17 UTC] PHP Notice: unserialize(): Error at offset 245 of 256 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:38:17 UTC] PHP Notice: unserialize(): Error at offset 245 of 256 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:38:20 UTC] PHP Notice: unserialize(): Error at offset 70 of 484 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:38:20 UTC] PHP Notice: unserialize(): Error at offset 70 of 484 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:38:32 UTC] PHP Notice: unserialize(): Error at offset 5563 of 7016 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:39:15 UTC] PHP Notice: unserialize(): Error at offset 146 of 278 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:39:15 UTC] PHP Notice: unserialize(): Error at offset 146 of 278 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:39:47 UTC] PHP Notice: unserialize(): Error at offset 42 of 186 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:39:47 UTC] PHP Notice: unserialize(): Error at offset 42 of 186 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:40:09 UTC] PHP Notice: unserialize(): Error at offset 73 of 115 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:40:09 UTC] PHP Notice: unserialize(): Error at offset 4620 of 4660 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:40:09 UTC] PHP Notice: unserialize(): Error at offset 89 of 4678 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:40:36 UTC] PHP Notice: unserialize(): Error at offset 59 of 204 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:40:36 UTC] PHP Notice: unserialize(): Error at offset 59 of 204 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:40:51 UTC] PHP Notice: unserialize(): Error at offset 194 of 312 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:40:52 UTC] PHP Notice: unserialize(): Error at offset 73 of 115 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:41:04 UTC] PHP Notice: unserialize(): Error at offset 440 of 458 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:41:04 UTC] PHP Notice: unserialize(): Error at offset 1153 of 1215 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:41:04 UTC] PHP Notice: unserialize(): Error at offset 442 of 460 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:41:09 UTC] PHP Notice: unserialize(): Error at offset 36 of 174 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:41:09 UTC] PHP Notice: unserialize(): Error at offset 36 of 174 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:41:24 UTC] PHP Notice: unserialize(): Error at offset 803 of 825 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:41:36 UTC] PHP Notice: unserialize(): Error at offset 40 of 178 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:41:36 UTC] PHP Notice: unserialize(): Error at offset 40 of 178 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:42:03 UTC] PHP Notice: unserialize(): Error at offset 90 of 404 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:42:17 UTC] PHP Notice: unserialize(): Error at offset 80 of 160 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:42:39 UTC] PHP Notice: unserialize(): Error at offset 1837 of 1930 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:42:52 UTC] PHP Notice: unserialize(): Error at offset 1203 of 1261 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:42:53 UTC] PHP Notice: unserialize(): Error at offset 4306 of 4464 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:43:38 UTC] PHP Notice: unserialize(): Error at offset 820 of 846 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:43:56 UTC] PHP Notice: unserialize(): Error at offset 1346 of 1499 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:43:56 UTC] PHP Notice: unserialize(): Error at offset 2436 of 11221 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347
[12-Dec-2016 10:44:01 UTC] PHP Notice: unserialize(): Error at offset 818 of 860 bytes in /dades/ojs/lib/pkp/classes/db/DAO.inc.php on line 347