diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index f6939394e6..cfdb4e9278 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -978,7 +978,7 @@ sub setup_cmdl_bgc {
   # Set soil matrix (which is needed later for spinup)
   $var = "use_soil_matrixcn";
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-              , 'use_fates'=>$nl_flags->{'use_fates'},
+              , 'use_fates'=>$nl_flags->{'use_fates'}, 
               , 'soil_decomp_method'=>$nl_flags->{'soil_decomp_method'},
               , 'phys'=>$nl_flags->{'phys'}, clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'} );
   if ( &value_is_true($nl->get_value($var)) ) {
@@ -1214,7 +1214,7 @@ sub setup_cmdl_spinup {
   if ( &value_is_true($nl_flags->{'use_cn'}) ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition,
                 $defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'},
-                use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'},
+                use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'}, 
                 use_soil_matrixcn=>$nl_flags->{"use_soil_matrixcn"} );
     if ( $nl->get_value("spinup_state") ne 0 ) {
        $nl_flags->{'bgc_spinup'} = "on";
@@ -1357,8 +1357,6 @@ sub setup_cmdl_run_type {
       $nl->set_variable_value($group, $var, quote_string( $opts->{$var} ) );
     }
   }
-  print "\n";
-  print "DEBUG0: clm_start_type is $nl_flags->{'clm_start_type'}\n";
   if ( ! defined $set ) {
      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
                  'use_cndv'=>$nl_flags->{'use_cndv'}, 'use_fates'=>$nl_flags->{'use_fates'},
@@ -1366,7 +1364,6 @@ sub setup_cmdl_run_type {
                  'bgc_spinup'=>$nl_flags->{'bgc_spinup'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
   }
   $nl_flags->{'clm_start_type'} = $nl->get_value($var);
-  print "DEBUG1: clm_start_type is $nl_flags->{'clm_start_type'}\n";
   $nl_flags->{'st_year'}        = $st_year;
 }
 
@@ -4153,6 +4150,10 @@ sub setup_logic_megan {
   if ( defined($nl->get_value('megan_specifier')) ||
          defined($nl->get_value('megan_factors_file')) ) {
     check_megan_spec( $opts, $nl, $definition );
+    if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
+      $log->warning("MEGAN can NOT be on when FATES is also on.\n" .
+                    "   Use the '-no-megan' option when '-bgc fates' is activated");
+    }
   }
 }
 
@@ -4965,7 +4966,7 @@ sub setup_logic_exice {
   # excess ice streams, must be set before initial conditions
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string());
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string()); 
   my $use_exice = $nl->get_value( 'use_excess_ice' );
   # Put use_exice into nl_flags so can be referenced later
   if ( value_is_true($use_exice) ) {
diff --git a/cime_config/buildnml b/cime_config/buildnml
index 414811abe6..e06b9388c7 100644
--- a/cime_config/buildnml
+++ b/cime_config/buildnml
@@ -75,8 +75,7 @@ def buildnml(case, caseroot, compname):
     run_reftod = case.get_value("RUN_REFTOD")
     start_tod = case.get_value("START_TOD")
     glc_nec = case.get_value("GLC_NEC")
-    cism_use_antarctica = case.get_value("CISM_USE_ANTARCTICA")
-    dglc_use_antarctica = case.get_value("DGLC_USE_ANTARCTICA")
+    glc_use_antarctica = case.get_value("GLC_USE_ANTARCTICA")
     mask = case.get_value("MASK_GRID")
     driver = case.get_value("COMP_INTERFACE").lower()
 
@@ -247,12 +246,9 @@ def buildnml(case, caseroot, compname):
     else:
         nomeg = ""
 
-    glc_use_antarctica = cism_use_antarctica
     if glc_use_antarctica is None:
-        glc_use_antarctica = dglc_use_antarctica
-    if glc_use_antarctica is None:
-        # This is the case for compsets without CISM or DGLC, where the
-        # CISM_USE_ANTARCTICA and DGLC_USE_ANTARCTICA xml variables are not defined
+        # This is the case for compsets with SGLC where the GLC_USE_ANTARCTICA xml
+        # variable isn't defined
         glc_use_antarctica_flag = ""
     elif isinstance(glc_use_antarctica, bool):
         if glc_use_antarctica:
@@ -260,16 +256,10 @@ def buildnml(case, caseroot, compname):
         else:
             glc_use_antarctica_flag = ""
     else:
-        if cism_use_antarctia:
-            expect(
-                False,
-                "Unexpected value for CISM_USE_ANTARCTICA: {}".format(cism_use_antarctica),
-            )
-        else:
-            expect(
-                False,
-                "Unexpected value for DGLC_USE_ANTARCTICA: {}".format(dglc_use_antarctica),
-            )
+        expect(
+            False,
+            "Unexpected value for GLC_USE_ANTARCTICA: {}".format(glc_use_antarctica),
+        )
 
     if clm_nml_use_case != "UNSET":
         usecase = "-use_case %s" % clm_nml_use_case