I recently restarted my whole server (gracefully) due to some cpu problems and all of my dbs returned empty.
2015-02-19T07:55:15.543+0100 [signalProcessingThread] got signal 15 (Terminated), will terminate after current cmd ends
2015-02-19T07:55:15.569+0100 [signalProcessingThread] now exiting
2015-02-19T07:55:15.569+0100 [signalProcessingThread] dbexit:
2015-02-19T07:55:15.569+0100 [signalProcessingThread] shutdown: going to close listening sockets...
2015-02-19T07:55:15.569+0100 [signalProcessingThread] closing listening socket: 8
2015-02-19T07:55:15.569+0100 [signalProcessingThread] closing listening socket: 9
2015-02-19T07:55:15.569+0100 [signalProcessingThread] removing socket file: /tmp/mongodb-27017.sock
2015-02-19T07:55:15.569+0100 [signalProcessingThread] shutdown: going to flush diaglog...
2015-02-19T07:55:15.569+0100 [signalProcessingThread] shutdown: going to close sockets...
2015-02-19T07:55:15.595+0100 [signalProcessingThread] shutdown: waiting for fs preallocator...
2015-02-19T07:55:15.595+0100 [signalProcessingThread] shutdown: lock for final commit...
2015-02-19T07:55:15.595+0100 [signalProcessingThread] shutdown: final commit...
...
2015-02-19T07:55:16.227+0100 [signalProcessingThread] shutdown: closing all files...
2015-02-19T07:55:16.227+0100 [signalProcessingThread] closeAllFiles() finished
2015-02-19T07:55:16.227+0100 [signalProcessingThread] journalCleanup...
2015-02-19T07:55:16.227+0100 [signalProcessingThread] removeJournalFiles
2015-02-19T07:55:16.932+0100 [signalProcessingThread] shutdown: removing fs lock...
2015-02-19T07:55:16.998+0100 [signalProcessingThread] dbexit: really exiting now
2015-02-19T07:58:00.082+0100 ***** SERVER RESTARTED *****
2015-02-19T07:58:00.161+0100 [initandlisten] MongoDB starting : pid=2571 port=27017 dbpath=/var/lib/mongo 64-bit host=
my.host.com2015-02-19T07:58:00.161+0100 [initandlisten] db version v2.6.5
2015-02-19T07:58:00.161+0100 [initandlisten] git version: e99d4fcb4279c0279796f237aa92fe3b64560bf6
2015-02-19T07:58:00.161+0100 [initandlisten] build info: Linux
build8.nj1.10gen.cc 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Jan 3 21:39:27 UTC 2014 x86_64 BOOST_LIB_VERSION=1_49
2015-02-19T07:58:00.161+0100 [initandlisten] allocator: tcmalloc
2015-02-19T07:58:00.161+0100 [initandlisten] options: { config: "/etc/mongod.conf", net: { bindIp: "127.0.0.1" }, processManagement: { fork: true, pidFilePath: "/var/run/mongodb/mongod.pid" }, storage: { dbPath: "/var/lib/mongo", directoryPerDB: true }, systemLog: { destination: "file", logAppend: true, path: "/var/log/mongodb/mongod.log" } }
2015-02-19T07:58:00.470+0100 [initandlisten] journal dir=/var/lib/mongo/journal
2015-02-19T07:58:00.470+0100 [initandlisten] recover : no journal files present, no recovery needed
2015-02-19T07:58:00.719+0100 [initandlisten] allocating new ns file /var/lib/mongo/local/local.ns, filling with zeroes...
2015-02-19T07:58:01.622+0100 [FileAllocator] allocating new datafile /var/lib/mongo/local/local.0, filling with zeroes...
2015-02-19T07:58:01.623+0100 [FileAllocator] creating directory /var/lib/mongo/local/_tmp
2015-02-19T07:58:01.854+0100 [FileAllocator] done allocating datafile /var/lib/mongo/local/local.0, size: 64MB, took 0.116 secs
2015-02-19T07:58:01.855+0100 [initandlisten] build index on: local.startup_log properties: { v: 1, key: { _id: 1 }, name: "_id_", ns: "local.startup_log" }
2015-02-19T07:58:01.855+0100 [initandlisten] added index to empty collection
2015-02-19T07:58:01.855+0100 [initandlisten] command local.$cmd command: create { create: "startup_log", size: 10485760, capped: true } ntoreturn:1 keyUpdates:0 numYields:0 reslen:37 1135ms
2015-02-19T07:58:01.855+0100 [initandlisten] waiting for connections on port 27017