code: private void failIndex(PhaseThreeOptions phasecfg, String errorMessage) {
          stageError(errorMessage);
          final StringBuilder bldr = new StringBuilder();
          bldr.append("Could not find resource index file.");
          bldr.append("Expansion of protein families, named complexes, ");
          bldr.append("gene scaffolding, and orthology will not occur.");
          stageError(bldr.toString());
          ResourceIndex.INSTANCE.loadIndex();
          phasecfg.setInjectProteinFamilies(false);
          phasecfg.setInjectNamedComplexes(false);
          phasecfg.setInjectGeneScaffolding(false);
          phasecfg.setInjectOrthology(false);
      }
docs: Logic to recover from a missing resource index.
  
  @param phasecfg
  @param errorMessage