The simplest explanation could be that the job you are re-running does not have the original inputs in the same history (actually deleted, or possibly in another history if these results are from a workflow, a copied histories, or similar). If this is your history or who shared it with you is willing to help, finding the original input and copying it into the history, or re-uploading, or undeleting (if not permanently deleted) may help. Although downstream problems may come up, see next..
If the Galaxy you are working on is functioning in other ways, a server problem seems unlikely to present this way. However, the GATK wrapper/tools themselves could present many unpredictable issues since these have been deprecated for a while and are no longer supported, updated, or undergoing new development by the prior key wrapper authors. Using GATK tools in Galaxy is not recommended. Specifically, any GATK tool's failure triggers increase if the version of Galaxy in use is a more recent release, as the wrappers are no longer tested/adjusted in response to the core platform's ongoing changes.
Instead, please see the alternative variant analysis workflows included here:
Take care, Jen, Galaxy team