A computer system having a transaction based file system is disclosed. The computer system includes file system software that manages the file data and the file system structure of files stored on a persistent data storage device and maintains a transaction file that includes a plurality of transaction records. The file system software executes a startup process in which a reconstructed file system is generated in random access memory from the transaction records. The startup process may skip verification of some of the transactions. The file system software may error check at least one of the skipped transactions in response to a request to access a file identified by a file node record in the reconstructed filed system after the startup process is completed.