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I had that issue with OSX 10.8.5 and both calibre 1.2 & 1.3/ I used time capsule backup to restore my calibre preferences file so I could start calibre.
File "site-packages/calibre/gui2/main.py", line 234, in initialize_db_stage2
File "site-packages/calibre/gui2/main.py", line 183, in start_gui
File "site-packages/calibre/gui2/ui.py", line 204, in initialize
File "site-packages/calibre/gui2/actions/__init__.py", line 142, in do_genesis
File "calibre_plugins.marvin_manager.action", line 126, in genesis
File "calibre_plugins.marvin_manager.action", line 257, in init_options
File "calibre_plugins.marvin_manager.annotations_db ", line 303, in connect
OperationalError: unable to open database file
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