Cron Job error "Could not open input file"
This is absurdly late to the game, but I did find a solution to this. What was happening was:
I had originally typed up the cron commands in Windows Notepad and uploaded them. Apparently what was happening was a carriage return ("/r", IIRC) was getting plugged in, unbeknownst to me (and vim, when I viewed the file from putty.) A friend removed those carriage returns by a method I don't recall/did not follow too well unfortunately, but after the returns were removed, it all worked.
Try this:
* * * * * cd /var/www/html/cron/; /usr/bin/php /var/www/html/cron/filename.php -q -f