There are NO viruses of any consequence for linux. There have been a few viruses released over the years, but none of them do anything unless you are running as root full time. The only reason programs like clam AV and f-prot exist is not to scan a linux box for viruses that would effect it, but to scan for viruses that would effect windows clients behind it. If your file server runs linux, and all the client computers are windows, it makes sense that the machine holding things should be certain that none of them can be harmful to the clients. Running AV on your linux box that isn't a server is an exercise in futility.
If you still insist on running this program, your errors are most likely caused because those files are in use. For the scan to go through you may have to leave the box alone. I have never used the program myself, so that is just a shot in the dark.