diff --git a/ksrates/fc_configfile.py b/ksrates/fc_configfile.py
index f73785624829f0274fff3ad3855e390e7cff0360..3e624c87c4e5b1b1f27a0f38e46b1df880efecbc 100644
--- a/ksrates/fc_configfile.py
+++ b/ksrates/fc_configfile.py
@@ -106,10 +106,10 @@ class Configuration:
         """
         species = self.config.get("SPECIES", "focal_species")
         if species == "":
-            logging.error("Parameter focal_species in configuration file is empty, please fill in")
+            logging.error('Parameter "focal_species" in configuration file is empty, please fill in')
             sys.exit(1)
         elif len(species.split()) != 1:
-            logging.error(f"Parameter focal_species [{species}] should be a short name and must not contain any spaces, please change accordingly")
+            logging.error(f'Parameter "focal_species" [{species}] should be a short name and must not contain any spaces, please change accordingly')
             sys.exit(1)
         return species
 
@@ -123,13 +123,13 @@ class Configuration:
         if not (tree_string.endswith(';')):
             tree_string += ";"
         if tree_string == "();":
-            logging.error("Parameter newick_tree in configuration file is empty, please fill in")
+            logging.error('Field "newick_tree" in configuration file is empty, please fill in')
             sys.exit(1)
         try:
             tree = Tree(tree_string)
             return tree
         except Exception:
-            logging.error("Unrecognized format for parameter newick_tree in configuration file (for example, parentheses do not match)")
+            logging.error('Unrecognized format for field "newick_tree" in configuration file (for example, parentheses do not match)')
             sys.exit(1)
 
     def check_complete_latin_names_dict(self, dictionary):
@@ -145,9 +145,9 @@ class Configuration:
         missing_species = list(set.difference(set(all_leaves), set(dictionary.keys())))
         if len(missing_species) != 0:
             if len(missing_species) == 1:
-                logging.error(f"The following species is missing from the [latin_names] configuration file field:")
+                logging.error(f'The following species is missing from the "latin_names" configuration file field:')
             else:
-                logging.error(f"The following species are missing from the [latin_names] configuration file field:")
+                logging.error(f'The following species are missing from the "latin_names" configuration file field:')
             for missing_name in missing_species:
                 logging.error(f" - {missing_name}")
             
@@ -165,7 +165,7 @@ class Configuration:
         if latin_names != "":
             latin_names_dict = self._get_clean_dict_stringent(latin_names, "latin_names")
         else:
-            logging.error("Configuration file field [latin_names] is empty, please fill in and restart the analysis.")
+            logging.error('Configuration file field "latin_names" is empty, please fill in and restart the analysis.')
             logging.error("Exiting.")
             sys.exit(1)
         # Check if latin_names contains all the species present in the Newick tree; if not, exits
@@ -466,6 +466,10 @@ class Configuration:
         """
         color_list_string = self.config.get("PARAMETERS", "divergence_colors")
         colors = [c.strip() for c in color_list_string.split(',')]
+        if len(colors) == 1 and colors[0] == "":
+            logging.error('Parameter "divergence_colors" in configuration file is empty, please fill in')
+            logging.error("Exiting.")
+            sys.exit(1)
         return colors
 
 
diff --git a/ksrates/setup_correction.py b/ksrates/setup_correction.py
index fd76ba1b21a063ce892a7a6284791e1022b07310..e659cf264adb6d859bd74efd17702fd198da0f57 100644
--- a/ksrates/setup_correction.py
+++ b/ksrates/setup_correction.py
@@ -24,6 +24,7 @@ def setup_correction(config_file, nextflow_flag):
     paranome = config.get_paranome()
     colinearity = config.get_colinearity()
     reciprocal_retention = config.get_reciprocal_retention()
+    divergence_colors = config.get_color_list()
 
     if not paranome and not colinearity and not reciprocal_retention:
         logging.error('At least one of the "paranome" or "collinearity" parameters in the configuration file needs to be set to "yes".')
@@ -104,15 +105,25 @@ def setup_correction(config_file, nextflow_flag):
         logging.error(f"Please add at least one outgroup species or change the focal species.")
         sys.exit(1)
 
+    # Obtaining the numeric labels for internal nodes relevant in the species analysis
+    fcTree.labeling_internal_nodes(species_of_interest_node)
+    # If the amount of colors provided for the divergence lines in the config file
+    # is insufficient for the number of divergence nodes in the tree, exit
+    num_required_colors = sp_history[-2].name
+    if len(divergence_colors) < num_required_colors:
+        logging.error("")
+        logging.error(f'Configuration file field "divergence_colors" is missing {num_required_colors - len(divergence_colors)} color(s) ' +
+                      f"out of {num_required_colors} required for the analysis on focal species [{species_of_interest}]")
+        logging.error("Please add the missing color(s) and rerun the analysis")
+        logging.error("Exiting.")
+        sys.exit(1)
+
     trios_array = []  # list of trios
     outfile_drawing_path = os.path.join("rate_adjustment", f"{species_of_interest}",
                                         f"tree_{species_of_interest}.txt")
     with open(outfile_drawing_path, "w+") as outfile_drawing:
         outfile_drawing.write(f"Focal species: {species_of_interest}\n\n")
 
-        # Obtaining the numeric labels for internal nodes relevant in the species analysis
-        fcTree.labeling_internal_nodes(species_of_interest_node)
-        
         node = 0
         while node < len(sp_history)-2:
             # the name label to be shown in the ASCII tree will start from 1 and not from 0