diff --git a/build.gradle b/build.gradle
index 15f8793f9..87780eb74 100644
--- a/build.gradle
+++ b/build.gradle
@@ -9,7 +9,7 @@ apply plugin: 'eclipse'
 
 sourceSets.main.java.srcDirs = ['src']
 mainClassName = "main.ScriptManager"
-version = 'v0.13-dev'
+version = 'v0.13'
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
 
diff --git a/src/main/ScriptManager.java b/src/main/ScriptManager.java
index 96485cb71..1937af6a4 100755
--- a/src/main/ScriptManager.java
+++ b/src/main/ScriptManager.java
@@ -70,7 +70,7 @@
 			Read_AnalysisCLI.class,
 			Sequence_AnalysisCLI.class
 		},
-		version = "ScriptManager-v0.13-dev",
+		version = "ScriptManager-v0.13",
 		mixinStandardHelpOptions = true,
 		description = "Choose a tool directory from below to see more command-line tool options.",
 		exitCodeOnInvalidInput = 1,
diff --git a/src/main/ScriptManagerGUI.java b/src/main/ScriptManagerGUI.java
index ef73b4cfa..421604740 100755
--- a/src/main/ScriptManagerGUI.java
+++ b/src/main/ScriptManagerGUI.java
@@ -55,7 +55,7 @@
 import window_interface.Figure_Generation.MergeHeatMapWindow;
 
 public class ScriptManagerGUI {
-	public static final String VERSION = "0.13-dev";
+	public static final String VERSION = "0.13";
 
 	private JFrame frmScriptManager;	
 	/**
diff --git a/src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java b/src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java
index c2b3a87c8..49b1815ce 100644
--- a/src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java
+++ b/src/window_interface/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFWindow.java
@@ -62,7 +62,7 @@ public Void doInBackground() throws IOException {
         		if(OUTPUT_PATH == null) OUT_FILE = new File( gffName );
         		else OUT_FILE = new File( OUTPUT_PATH + File.separator + gffName );
         		// Execute conversion and update progress
-				BEDtoGFF.convertBEDtoGFF(OUTPUT_PATH, XBED);
+			BEDtoGFF.convertBEDtoGFF(OUT_FILE, XBED);
 				int percentComplete = (int)(((double)(x + 1) / BEDFiles.size()) * 100);
         		setProgress(percentComplete);
         	}
@@ -197,4 +197,4 @@ public void massXable(Container con, boolean status) {
 			if(c instanceof Container) { massXable((Container)c, status); }
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFWindow.java b/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFWindow.java
index cf0775563..d0bfe73e1 100644
--- a/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFWindow.java
+++ b/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFWindow.java
@@ -76,8 +76,8 @@ public Void doInBackground() throws IOException {
 		        		File OUT_FILE = null;
 		        		if(OUTPUT_PATH == null) OUT_FILE = new File( newName );
 		        		else OUT_FILE = new File( OUTPUT_PATH + File.separator + newName );
-						// Execute expansion and update progress
-		        		ExpandGFF.expandGFFBorders(OUTPUT_PATH, XGFF, SIZE, rdbtnExpandFromCenter.isSelected());
+					// Execute expansion and update progress
+		        		ExpandGFF.expandGFFBorders(OUT_FILE, XGFF, SIZE, rdbtnExpandFromCenter.isSelected());
 						int percentComplete = (int)(((double)(x + 1) / GFFFiles.size()) * 100);
 		        		setProgress(percentComplete);
 		        	}
@@ -245,4 +245,4 @@ public void massXable(Container con, boolean status) {
 			if(c instanceof Container) { massXable((Container)c, status); }
 		}
 	}
-}
\ No newline at end of file
+}
diff --git a/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java b/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java
index 229c74a7d..3f3364444 100644
--- a/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java
+++ b/src/window_interface/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDWindow.java
@@ -62,7 +62,7 @@ public Void doInBackground() throws IOException {
 				if(OUTPUT_PATH == null) OUT_FILE = new File( bedName );
 				else OUT_FILE = new File( OUTPUT_PATH + File.separator + bedName );
 				// Execute conversion and update progress
-	    		GFFtoBED.convertGFFtoBED(OUTPUT_PATH, XGFF);
+	    		GFFtoBED.convertGFFtoBED(OUT_FILE, XGFF);
 				int percentComplete = (int)(((double)(x + 1) / BEDFiles.size()) * 100);
         		setProgress(percentComplete);
         	}
@@ -197,4 +197,4 @@ public void massXable(Container con, boolean status) {
 			if(c instanceof Container) { massXable((Container)c, status); }
 		}
 	}
-}
\ No newline at end of file
+}