Is the dataset in the same history as you are running the job? Is the metadata set correctly (datatype, database)?
Also, where are you working .. the public Main Galaxy instance at http://usegalaxy.org or somewhere else? If somewhere else and the data is labeled correctly (usually necessary for the datasets to be selected from the tool form), this is most likely a file system issue, and the local administrator of the instance would be the one to help.
Thanks, Jen, Galaxy team