diff --git a/classes/Mission.m b/classes/Mission.m
index 2694c76e83ce1712ebf9242cc469df34a12a58da..f505cd8248e23e677770f3a0954924074d295f9d 100644
--- a/classes/Mission.m
+++ b/classes/Mission.m
@@ -65,7 +65,7 @@ classdef Mission < Config
             obj.configPath = fullfile(obj.currentPath, obj.name, 'config');
             obj.dataPath = fullfile(obj.currentPath, obj.name, 'data');
             obj.msaPath = trimPath( ...
-                fullfile(obj.currentPath, '..', '..', 'msa-toolkit') ...
+                fullfile(obj.currentPath, '..', '..', '..', 'msa-toolkit') ...
                 );
         end
 
diff --git a/functions/miscellaneous/trimPath.m b/functions/miscellaneous/trimPath.m
index 192009c56937b775992d604a9bf0efc661d5f8fb..1fe4dd67a84f9dacb0020c8d5d0c08f7df01d014 100644
--- a/functions/miscellaneous/trimPath.m
+++ b/functions/miscellaneous/trimPath.m
@@ -13,7 +13,7 @@ out = fullfile(path); % Trims multiple separators characters
 exp = ['\', filesep, '[^\', filesep,']+\', filesep,'\.\.'];
 
 while ~trimmed
-    out = regexprep(out, exp, '');
+    out = regexprep(out, exp, '', 'once');
     trimmed = ~logical(regexp(out, exp, 'once'));
 end