What parameters did you use with chkdsk? If none, then I would stop it, and start it again using chkdsk /r and do so from an elevated command prompt (As administrator). And note on large drives, it can take a long time, hours, even overnight to complete. So as softwaremaniac advises, let it run until completion.
Note it is safe to stop chkdsk if it was started with no parameters because that is running in read-only mode. If you used /r or /f, for example, then it runs in read-write mode and it is best to let it complete or risk disk corruption.