}else{ filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); }
}
- filename += "groups";
+ //prevent giantic file name
+ if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
+ else { filename += "groups"; }
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }