At line 2627 of org.dllearner.reasoning.SPARQLReasoner.executeSelectQuery, the deprecated Jena method qe.setTimeout(timeout, timeoutUnits) is called.
As seen in the Jena code here, this method is deprecated. This leads to an java.lang.UnsupportedOperationException: Not Implemented. error thrown by the Jena code.
This error is preventing the SPARQLReasoner class from being able to launch queries against a remote endpoint.