The aligner was given a reference that has no index beside it
Aligners take the prefix of an index and expect the generated index files to sit in the same directory under that same prefix. If the index was built elsewhere, only some files were staged, or the prefix does not match what was indexed, the aligner cannot assemble the set — and typically dumps its whole usage text, which makes it look like a syntax error instead.
List the directory and confirm the full index set is next to the reference, all sharing one prefix. In a workflow, check what the indexing step actually staged into the task's working directory: the file passed to the aligner and the file that was indexed must be the same prefix.