if (followUpCLIInputBean.inclusionListNeeded()) {
try {
CLIMethods.exportInclusionList(followUpCLIInputBean, identification, identificationFeaturesGenerator, identificationParameters.getSearchParameters(), waitingHandler, filterPreferences);
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while generating the inclusion list.", true, true);
<BUG>e.printStackTrace();
}</BUG>
}
try {
<BUG>closePeptideShaker();
} catch (Exception e) {
</BUG>
waitingHandler.appendReport("An error occurred while closing PeptideShaker.", true, true);

if (followUpCLIInputBean.inclusionListNeeded()) {
try {
CLIMethods.exportInclusionList(followUpCLIInputBean, identification, identificationFeaturesGenerator, identificationParameters.getSearchParameters(), waitingHandler, filterPreferences);
