diff --git a/gui/checkthread.cpp b/gui/checkthread.cpp
index d46a75f88..14fd14bf2 100644
--- a/gui/checkthread.cpp
+++ b/gui/checkthread.cpp
@@ -108,13 +108,10 @@ void CheckThread::run()
     if (!mFiles.isEmpty() || mAnalyseWholeProgram) {
         mAnalyseWholeProgram = false;
         qDebug() << "Whole program analysis";
-        const std::string &buildDir = mCppcheck.settings().buildDir;
-        if (!buildDir.empty()) {
-            std::map<std::string,std::size_t> files2;
-            for (const QString& file : mFiles)
-                files2[file.toStdString()] = 0;
-            mCppcheck.analyseWholeProgram(buildDir, files2);
-        }
+        std::map<std::string,std::size_t> files2;
+        for (const QString& file : mFiles)
+            files2[file.toStdString()] = 0;
+        mCppcheck.analyseWholeProgram(mCppcheck.settings().buildDir, files2);
         mFiles.clear();
         emit done();
         return;
diff --git a/lib/cppcheck.cpp b/lib/cppcheck.cpp
index 58c4fa719..0cf3635d0 100644
--- a/lib/cppcheck.cpp
+++ b/lib/cppcheck.cpp
@@ -1759,8 +1759,10 @@ bool CppCheck::analyseWholeProgram()
 void CppCheck::analyseWholeProgram(const std::string &buildDir, const std::map<std::string, std::size_t> &files)
 {
     executeAddonsWholeProgram(files);
-    if (buildDir.empty())
+    if (buildDir.empty()) {
+        removeCtuInfoFiles(files);
         return;
+    }
     if (mSettings.checks.isEnabled(Checks::unusedFunction))
         CheckUnusedFunctions::analyseWholeProgram(this, buildDir);
     std::list<Check::FileInfo*> fileInfoList;
@@ -1821,3 +1823,14 @@ bool CppCheck::isUnusedFunctionCheckEnabled() const
 {
     return (mSettings.jobs == 1 && mSettings.checks.isEnabled(Checks::unusedFunction));
 }
+
+void CppCheck::removeCtuInfoFiles(const std::map<std::string, std::size_t> &files)
+{
+    if (mSettings.buildDir.empty()) {
+        for (const auto& f: files) {
+            const std::string &dumpFileName = getDumpFileName(mSettings, f.first);
+            const std::string &ctuInfoFileName = getCtuInfoFileName(dumpFileName);
+            std::remove(ctuInfoFileName.c_str());
+        }
+    }
+}
diff --git a/lib/cppcheck.h b/lib/cppcheck.h
index 5889b63dd..fe9c8187c 100644
--- a/lib/cppcheck.h
+++ b/lib/cppcheck.h
@@ -145,6 +145,9 @@ public:
      * and if it's possible at all */
     bool isUnusedFunctionCheckEnabled() const;
 
+    /** Remove *.ctu-info files */
+    void removeCtuInfoFiles(const std::map<std::string, std::size_t>& files);
+
 private:
     /** Are there "simple" rules */
     bool hasRule(const std::string &tokenlist) const;