Well, your database is definitely corrupted.
Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Database optimization: Optimizing database. Starting by capturing all sessions. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 0. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 1. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 2. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 3. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 4. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 5. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 6. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 7. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 8. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 9. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 10. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 11. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 12. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 13. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 14. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 15. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 16. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 17. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 18. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Captured session 19. Jan 08, 2017 15:34:04.853 [0x700004110000] DEBUG - Database optimization: Rebuilding full text search tables. Jan 08, 2017 15:34:05.769 [0x700004110000] WARN - Held transaction for too long (../Library/FullTextSearch.cpp:16): 0.880000 seconds Jan 08, 2017 15:34:06.406 [0x700004110000] WARN - Held transaction for too long (../Library/FullTextSearch.cpp:26): 0.610000 seconds Jan 08, 2017 15:34:06.916 [0x700004110000] ERROR - SQLITE3:0x70000385c0d0, 11, database corruption at line 59437 of [fc49f556e4] Jan 08, 2017 15:34:06.916 [0x700004110000] ERROR - SQLITE3:0x70000385c0d0, 11, database corruption at line 59479 of [fc49f556e4] Jan 08, 2017 15:34:06.916 [0x700004110000] ERROR - SQLITE3:0x70000385c0d0, 11, statement aborts at 4: [] database disk image is malformed Jan 08, 2017 15:34:06.918 [0x700004110000] ERROR - SQLITE3:0x70000385c0d0, 11, statement aborts at 36: [insert into fts4_tag_titles(rowid, tag) select id, tag from tags where tag_type in (1,4,6)] database disk image is malformed Jan 08, 2017 15:34:06.918 [0x700004110000] ERROR - Exception inside transaction (inside=1) (../Library/FullTextSearch.cpp:35): sqlite3_statement_backend::loadOne: database disk image is malformed Jan 08, 2017 15:34:06.926 [0x700004110000] ERROR - Soci Exception handled: sqlite3_statement_backend::loadOne: database disk image is malformed
I’m unsure of how to repair the database. Have to wait for a ninja or other SQLITE knowledgeable person to comment on that.