if(!out) {
mothurOut(output + " directory does not exist or is not writable."); mothurOutEndLine();
}else{
+ out.close();
remove(outTemp.c_str());
mothurOut("Changing output directory to " + output); mothurOutEndLine();
commandFactory->setOutputDirectory(output);
if(!in) {
mothurOut(input + " directory does not exist or is not writable."); mothurOutEndLine();
}else{
+ in.close();
remove(inTemp.c_str());
mothurOut("Changing input directory to " + input); mothurOutEndLine();
commandFactory->setInputDirectory(input);