Index: src/corelibs/U2Core/src/globals/ExternalToolRegistry.cpp
===================================================================
--- src/corelibs/U2Core/src/globals/ExternalToolRegistry.cpp	(revision 9446)
+++ src/corelibs/U2Core/src/globals/ExternalToolRegistry.cpp	(working copy)
@@ -69,6 +69,10 @@
 #endif
 }
 
+void ExternalTool::actionsAfterValidationStarts(){
+
+}
+
 ////////////////////////////////////////
 //ExternalToolValidationListener
 ExternalToolValidationListener::ExternalToolValidationListener(const QString& toolName) {
Index: src/corelibs/U2Core/src/globals/ExternalToolRegistry.h
===================================================================
--- src/corelibs/U2Core/src/globals/ExternalToolRegistry.h	(revision 9446)
+++ src/corelibs/U2Core/src/globals/ExternalToolRegistry.h	(working copy)
@@ -88,6 +88,8 @@
     bool isValid() const { return isValidTool; }
     bool isMuted() const;
     bool isModule() const { return isModuleTool; }
+
+    virtual void actionsAfterValidationStarts();
 signals:
     void si_pathChanged();
     void si_toolValidationStatusChanged(bool isValid);
Index: src/plugins/external_tool_support/src/fastqc/FastqcSupport.cpp
===================================================================
--- src/plugins/external_tool_support/src/fastqc/FastqcSupport.cpp	(revision 9446)
+++ src/plugins/external_tool_support/src/fastqc/FastqcSupport.cpp	(working copy)
@@ -19,6 +19,8 @@
  * MA 02110-1301, USA.
  */
 
+#include <QElapsedTimer>
+
 #include "FastqcSupport.h"
 #include "java/JavaSupport.h"
 #include "perl/PerlSupport.h"
@@ -58,5 +60,13 @@
     dependencies << ET_PERL;
 }
 
+void FastQCSupport::actionsAfterValidationStarts(){
+#ifdef Q_OS_WIN
+    QElapsedTimer timer;
+    timer.start();
+    while(timer.elapsed() < 1000);
+#endif
+}
+
 }//namespace
 
Index: src/plugins/external_tool_support/src/fastqc/FastqcSupport.h
===================================================================
--- src/plugins/external_tool_support/src/fastqc/FastqcSupport.h	(revision 9446)
+++ src/plugins/external_tool_support/src/fastqc/FastqcSupport.h	(working copy)
@@ -33,6 +33,7 @@
 public:
     FastQCSupport(const QString& name, const QString& path = "");
 
+    virtual void actionsAfterValidationStarts();
 };
 
 }//namespace
Index: src/plugins/external_tool_support/src/utils/ExternalToolValidateTask.cpp
===================================================================
--- src/plugins/external_tool_support/src/utils/ExternalToolValidateTask.cpp	(revision 9446)
+++ src/plugins/external_tool_support/src/utils/ExternalToolValidateTask.cpp	(working copy)
@@ -133,7 +133,7 @@
             isValid = false;
             return;
         }
-
+        tool->actionsAfterValidationStarts();
         while (!externalToolProcess->waitForFinished(1000)) {
             if (isCanceled()) {
                 cancelProcess();