No input file specified - htaccess and /?/ after base_url

Hosting provider updated their server today to PHP 5.6.25. After the update, all pages (except homepage) of my website just throw the error: No input file specified. After check on internet I found the solution: Add question mark in .htaccess file

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ ./index.php?/$1 [L,QSA]

It make the website work again but I'm facing the other problem now, all the urls of my website turn from
http://abc.com/omega
to
http://abc.com/?/omega
I'm stucked now, so please help.