diff --git a/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoBEDCLI.java b/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoBEDCLI.java
index 65aaab0d..3752192d 100644
--- a/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoBEDCLI.java
+++ b/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoBEDCLI.java
@@ -106,10 +106,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -128,12 +124,6 @@ private String validateInput() throws IOException {
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!"bed".equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use BED extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".bed\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use BED extension for output filename. Try: " + output + ".bed\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoGFFCLI.java b/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoGFFCLI.java
index 1fc5e1e3..e98cfab0 100644
--- a/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoGFFCLI.java
+++ b/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoGFFCLI.java
@@ -106,10 +106,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -128,12 +124,6 @@ private String validateInput() throws IOException {
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!"gff".equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use GFF extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".gff\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use GFF extension for output filename. Try: " + output + ".gff\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtobedGraphCLI.java b/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtobedGraphCLI.java
index 36ac1620..a85ed774 100644
--- a/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtobedGraphCLI.java
+++ b/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtobedGraphCLI.java
@@ -101,10 +101,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
diff --git a/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoscIDXCLI.java b/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoscIDXCLI.java
index 143093bc..269ac5d2 100644
--- a/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoscIDXCLI.java
+++ b/src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoscIDXCLI.java
@@ -103,10 +103,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -125,12 +121,6 @@ private String validateInput() throws IOException {
 			if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!"tab".equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use \".tab\" extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".tab\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use \".tab\" extension for output filename. Try: " + output + ".tab\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/BAM_Manipulation/FilterforPIPseqCLI.java b/src/main/java/scriptmanager/cli/BAM_Manipulation/FilterforPIPseqCLI.java
index 29ee457e..cfe64640 100644
--- a/src/main/java/scriptmanager/cli/BAM_Manipulation/FilterforPIPseqCLI.java
+++ b/src/main/java/scriptmanager/cli/BAM_Manipulation/FilterforPIPseqCLI.java
@@ -80,14 +80,6 @@ private String validateInput() throws IOException {
 		if (!r.equals("")) {
 			return (r);
 		}
-		// check input extensions
-		ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
-		if (!faFilter.accept(genomeFASTA)) {
-			r += "(!)Is this a FASTA file? Check extension: " + genomeFASTA.getName() + "\n";
-		}
-		if (!"bam".equals(ExtensionFileFilter.getExtension(bamFile))) {
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		// check BAI exists
 		File f = new File(bamFile + ".bai");
 		if (!f.exists() || f.isDirectory()) {
@@ -105,16 +97,6 @@ private String validateInput() throws IOException {
 			output = new File(ExtensionFileFilter.stripExtension(bamFile) + "_PSfilter.bam");
 			// check output filename is valid
 		} else {
-			// check ext
-			try {
-				if (!"bam".equals(ExtensionFileFilter.getExtension(output))) {
-					r += "(!)Use BAM extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
-							+ ".bam\n";
-				}
-			} catch (NullPointerException e) {
-				r += "(!)Output filename must have extension: use BAM extension for output filename. Try: "
-						+ ExtensionFileFilter.stripExtension(output) + ".bam\n";
-			}
 			// check directory
 			if (output.getParent() == null) {
 // 					System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/BAM_Statistics/BAMGenomeCorrelationCLI.java b/src/main/java/scriptmanager/cli/BAM_Statistics/BAMGenomeCorrelationCLI.java
index 4c7aa85f..6ae1d91b 100644
--- a/src/main/java/scriptmanager/cli/BAM_Statistics/BAMGenomeCorrelationCLI.java
+++ b/src/main/java/scriptmanager/cli/BAM_Statistics/BAMGenomeCorrelationCLI.java
@@ -135,9 +135,6 @@ private String validateInput() throws IOException {
 			//check input exists
 			if(!BAM.exists()|| BAM.isDirectory()){
 				r += "(!)BAM[" + x + "] file does not exist: " + BAM.getName() + "\n";
-			//check input extensions
-			}else if(!"bam".equals(ExtensionFileFilter.getExtension(BAM))){
-				r += "(!)Is this a BAM file? Check extension: " + BAM.getName() + "\n";
 			//check BAI exists
 			}else if(!BAI.exists() || BAI.isDirectory()){
 				r += "(!)BAI Index File does not exist for: " + BAM.getName() + "\n";
@@ -149,7 +146,6 @@ private String validateInput() throws IOException {
 			outputBasename = new File("correlation_matrix");
 		//check output filename is valid
 		}else{
-			//no check ext
 			//check directory
 			if(outputBasename.getParent()==null){
 // 				System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/BAM_Statistics/PEStatsCLI.java b/src/main/java/scriptmanager/cli/BAM_Statistics/PEStatsCLI.java
index 65cdd917..c2c17fb6 100644
--- a/src/main/java/scriptmanager/cli/BAM_Statistics/PEStatsCLI.java
+++ b/src/main/java/scriptmanager/cli/BAM_Statistics/PEStatsCLI.java
@@ -69,10 +69,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -84,7 +80,6 @@ private String validateInput() throws IOException {
 			outputBasename = new File(ExtensionFileFilter.stripExtension(bamFile));
 		//check output filename is valid
 		}else{
-			//no check ext
 			//check directory
 			if(outputBasename.getParent()==null){
 // 				System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/BAM_Statistics/SEStatsCLI.java b/src/main/java/scriptmanager/cli/BAM_Statistics/SEStatsCLI.java
index 98140802..6ea727af 100644
--- a/src/main/java/scriptmanager/cli/BAM_Statistics/SEStatsCLI.java
+++ b/src/main/java/scriptmanager/cli/BAM_Statistics/SEStatsCLI.java
@@ -61,10 +61,6 @@ private String validateInput() throws IOException {
 			r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
-		}
 		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
@@ -76,7 +72,6 @@ private String validateInput() throws IOException {
 			output = new File(ExtensionFileFilter.stripExtension(bamFile) + "_stats.txt");
 		//check output filename is valid
 		}else{
-			//no check ext
 			//check directory
 			if(output.getParent()==null){
 // 				System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/Figure_Generation/MergeHeatMapCLI.java b/src/main/java/scriptmanager/cli/Figure_Generation/MergeHeatMapCLI.java
index 16330b8a..e65acc7d 100644
--- a/src/main/java/scriptmanager/cli/Figure_Generation/MergeHeatMapCLI.java
+++ b/src/main/java/scriptmanager/cli/Figure_Generation/MergeHeatMapCLI.java
@@ -38,8 +38,7 @@ public MergeHeatMapCLI(){}
 	@Parameters(index = "1", description = "Second(anti) PNG heatmap to merge, input2")
 	private File antiFile;
 
-	@Option(names = { "-o",
-			"--output" }, description = "specify output filename, please use PNG extension\n(default=\"<senseFile>_merged.png\" appended to the name in working directory of ScriptManager")
+	@Option(names = { "-o", "--output" }, description = "specify output filename, please use PNG extension\n(default=\"<senseFile>_merged.png\" appended to the name in working directory of ScriptManager")
 	private File output = null;
 
 	/**
@@ -76,29 +75,12 @@ private String validateInput() throws IOException {
 		if (!r.equals("")) {
 			return (r);
 		}
-		// check input extensions
-		if (!"png".equals(ExtensionFileFilter.getExtension(senseFile))) {
-			r += "(!)Is this a PNG file? Check extension: " + senseFile.getName() + "\n";
-		}
-		if (!"png".equals(ExtensionFileFilter.getExtension(antiFile))) {
-			r += "(!)Is this a PNG file? Check extension: " + antiFile.getName() + "\n";
-		}
 		// set default output filename
 		if (output == null) {
 			String NAME = ExtensionFileFilter.stripExtension(senseFile);
 			output = new File(NAME + "_merged.png");
 			// check output filename is valid
 		} else {
-			// check ext
-			try {
-				if (!"png".equals(ExtensionFileFilter.getExtension(output))) {
-					r += "(!)Use PNG extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
-							+ ".png\n";
-				}
-			} catch (NullPointerException e) {
-				r += "(!)Output filename must have extension: use PNG extension for output filename. Try: " + output
-						+ ".png\n";
-			}
 			// check directory
 			if (output.getParent() == null) {
 // 				System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/Figure_Generation/ThreeColorHeatMapCLI.java b/src/main/java/scriptmanager/cli/Figure_Generation/ThreeColorHeatMapCLI.java
index d29a706b..988d1d31 100644
--- a/src/main/java/scriptmanager/cli/Figure_Generation/ThreeColorHeatMapCLI.java
+++ b/src/main/java/scriptmanager/cli/Figure_Generation/ThreeColorHeatMapCLI.java
@@ -171,26 +171,12 @@ private String validateInput() throws IOException {
 			r += "(!)CDT file does not exist: " + CDT.getName() + "\n";
 			return (r);
 		}
-		// check input extensions
-		if (!"cdt".equals(ExtensionFileFilter.getExtension(CDT))) {
-			r += "(!)Is this a CDT file? Check extension: " + CDT.getName() + "\n";
-		}
 		// set default output filename
 		if (output == null) {
 			String NAME = ExtensionFileFilter.stripExtension(CDT);
 			output = new File(NAME + "_" + scaleType + ".png");
 			// check output filename is valid
 		} else {
-			// check ext
-			try {
-				if (!"png".equals(ExtensionFileFilter.getExtension(output))) {
-					r += "(!)Use PNG extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
-							+ ".png\n";
-				}
-			} catch (NullPointerException e) {
-				r += "(!)Output filename must have extension: use PNG extension for output filename. Try: " + output
-						+ ".png\n";
-			}
 			// check directory
 			if (output.getParent() == null) {
 // 				System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/Peak_Analysis/BEDPeakAligntoRefCLI.java b/src/main/java/scriptmanager/cli/Peak_Analysis/BEDPeakAligntoRefCLI.java
index 9f9bb10c..188a272b 100644
--- a/src/main/java/scriptmanager/cli/Peak_Analysis/BEDPeakAligntoRefCLI.java
+++ b/src/main/java/scriptmanager/cli/Peak_Analysis/BEDPeakAligntoRefCLI.java
@@ -71,24 +71,11 @@ private String validateInput() throws IOException {
 			r += "(!)BED-ref file does not exist: " + refBED.getName() + "\n";
 		}
 		if(!r.equals("")){ return(r); }
-		//check input extensions
-		if(!"bed".equals(ExtensionFileFilter.getExtension(peakBED))){
-			r += "(!)Is this a BED file? Check extension: " + peakBED.getName() + "\n";
-		}
-		if(!"bed".equals(ExtensionFileFilter.getExtension(refBED))){
-			r += "(!)Is this a BED file? Check extension: " + refBED.getName() + "\n";
-		}
 		//set default output filename
 		if(output==null){
 			output = new File(ExtensionFileFilter.stripExtension(peakBED) + "_" + ExtensionFileFilter.stripExtension(refBED) + "_Output.cdt");
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!"cdt".equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use CDT extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".cdt\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use CDT extension for output filename. Try: " + output + ".cdt\n"; }
 			//check directory
 			if(output.getParent()==null){
 // 				System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/Peak_Analysis/FilterBEDbyProximityCLI.java b/src/main/java/scriptmanager/cli/Peak_Analysis/FilterBEDbyProximityCLI.java
index c777a10a..652582ee 100644
--- a/src/main/java/scriptmanager/cli/Peak_Analysis/FilterBEDbyProximityCLI.java
+++ b/src/main/java/scriptmanager/cli/Peak_Analysis/FilterBEDbyProximityCLI.java
@@ -64,16 +64,11 @@ private String validateInput() throws IOException {
 			r += "(!)BED file does not exist: " + bedFile.getName() + "\n";
 			return(r);
 		}
-		//check input extensions
-		if(!"bed".equals(ExtensionFileFilter.getExtension(bedFile))){
-			r += "(!)Is this a BED file? Check extension: " + bedFile.getName() + "\n";
-		}
 		//set default output filename
 		if(outputBasename==null){
 			outputBasename = ExtensionFileFilter.stripExtension(bedFile) + "_" + Integer.toString(exclusion) + "bp";
 		//check output filename is valid
 		}else{
-			//no check ext
 			//check directory
 			File tmpOut = new File(outputBasename);
 			if(tmpOut.getParent()==null){
diff --git a/src/main/java/scriptmanager/cli/Peak_Analysis/RandomCoordinateCLI.java b/src/main/java/scriptmanager/cli/Peak_Analysis/RandomCoordinateCLI.java
index 92471edc..97f0e27e 100644
--- a/src/main/java/scriptmanager/cli/Peak_Analysis/RandomCoordinateCLI.java
+++ b/src/main/java/scriptmanager/cli/Peak_Analysis/RandomCoordinateCLI.java
@@ -69,12 +69,6 @@ private String validateInput() throws IOException {
 			output = new File("random_coordinates_" + genomeName + "_" + numSites + "sites_" + window + "bp." + ext);
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!ext.equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + "." + ext + "\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + output + "." + ext + "\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/Peak_Analysis/TileGenomeCLI.java b/src/main/java/scriptmanager/cli/Peak_Analysis/TileGenomeCLI.java
index c774c8fe..bdfdfd30 100644
--- a/src/main/java/scriptmanager/cli/Peak_Analysis/TileGenomeCLI.java
+++ b/src/main/java/scriptmanager/cli/Peak_Analysis/TileGenomeCLI.java
@@ -67,12 +67,6 @@ private String validateInput() throws IOException {
 			output = new File(genomeName + "_" + window + "bp." + ext);
 		//check output filename is valid
 		}else{
-			//check ext
-			try{
-				if(!ext.equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + "." + ext + "\n";
-				}
-			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + output + "." + ext + "\n"; }
 			//check directory
 			if(output.getParent()==null){
 	// 			System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/Read_Analysis/ScalingFactorCLI.java b/src/main/java/scriptmanager/cli/Read_Analysis/ScalingFactorCLI.java
index b9be7001..db30c9d3 100644
--- a/src/main/java/scriptmanager/cli/Read_Analysis/ScalingFactorCLI.java
+++ b/src/main/java/scriptmanager/cli/Read_Analysis/ScalingFactorCLI.java
@@ -93,19 +93,11 @@ private String validateInput() throws IOException {
 			if(!controlBAM.exists()){ r += "(!)BAM(control) file does not exist: " + controlBAM.getName() + "\n"; }
 		}
 		if(!r.equals("")){ return(r); }
-		//check input extensions & BAI exists
-		if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
-			r += "(!)Is this a BAM(input) file? Check extension: " + bamFile.getName() + "\n";
-		}
+		//check BAI exists
 		File f = new File(bamFile+".bai");
 		if(!f.exists() || f.isDirectory()){
 			r += "(!)BAI Index File does not exist for: " + bamFile.getName() + "\n";
 		}
-		if(blacklistFilter!=null){
-			if(!"bed".equals(ExtensionFileFilter.getExtension(blacklistFilter))){
-				r += "(!)Is this a BED file? Check extension: " + blacklistFilter.getName() + "\n";
-			}
-		}
 		if(controlBAM!=null){
 			if(!"bam".equals(ExtensionFileFilter.getExtension(controlBAM))){
 				r += "(!)Is this a BAM(control) file? Check extension: " + controlBAM.getName() + "\n";
@@ -121,7 +113,6 @@ private String validateInput() throws IOException {
 		//check output filename is valid
 		}else{
 			File tempOut = new File(outputBasename);
-			//no check ext
 			//check directory
 			if(tempOut.getParent()==null){
 // 				System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/Read_Analysis/TagPileupCLI.java b/src/main/java/scriptmanager/cli/Read_Analysis/TagPileupCLI.java
index 3e897199..0458e9b5 100644
--- a/src/main/java/scriptmanager/cli/Read_Analysis/TagPileupCLI.java
+++ b/src/main/java/scriptmanager/cli/Read_Analysis/TagPileupCLI.java
@@ -198,7 +198,6 @@ private String validateInput() throws IOException {
 		//check output COMPOSITE filename is valid
 		if(outputOptions.outputComposite!="composite_average.out"){
 			File output = new File(outputOptions.outputComposite);
-			//no check ext
 			//check directory
 			if(output.getParent()==null){
 // 				System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromBEDCLI.java b/src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromBEDCLI.java
index b5f1b83a..1d52d6d0 100644
--- a/src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromBEDCLI.java
+++ b/src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromBEDCLI.java
@@ -131,14 +131,6 @@ private String validateInput() throws IOException {
 		if (!r.equals("")) {
 			return (r);
 		}
-		// check input extensions
-		ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
-		if (!faFilter.accept(genomeFASTA)) {
-			r += "(!)Is this a FASTA file? Check extension: " + genomeFASTA.getName() + "\n";
-		}
-		if (!"bed".equals(ExtensionFileFilter.getExtension(bedFile))) {
-			r += "(!)Is this a BED file? Check extension: " + bedFile.getName() + "\n";
-		}
 		// set default output filename
 		if (outputBasename == null) {
 			outputBasename = ExtensionFileFilter.stripExtension(bedFile);
diff --git a/src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromFASTACLI.java b/src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromFASTACLI.java
index 88a546bb..cbe9ce35 100644
--- a/src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromFASTACLI.java
+++ b/src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromFASTACLI.java
@@ -125,18 +125,12 @@ private String validateInput() throws IOException {
 			r += "(!)FASTA file does not exist: " + fastaFile.getName() + "\n";
 			return (r);
 		}
-		// check input extensions
-		ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
-		if (!faFilter.accept(fastaFile)) {
-			r += "(!)Is this a FASTA file? Check extension: " + fastaFile.getName() + "\n";
-		}
 		// set default output filename
 		if (outputBasename == null) {
 			outputBasename = ExtensionFileFilter.stripExtension(fastaFile);
 			// check output filename is valid
 		} else {
 			String outParent = new File(outputBasename).getParent();
-			// no extension check
 			// check directory
 			if (outParent == null) {
 // 				System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/Sequence_Analysis/RandomizeFASTACLI.java b/src/main/java/scriptmanager/cli/Sequence_Analysis/RandomizeFASTACLI.java
index fa16b8d4..a2c81e63 100644
--- a/src/main/java/scriptmanager/cli/Sequence_Analysis/RandomizeFASTACLI.java
+++ b/src/main/java/scriptmanager/cli/Sequence_Analysis/RandomizeFASTACLI.java
@@ -70,27 +70,12 @@ private String validateInput() throws IOException {
 			r += "(!)FASTA file does not exist: " + fastaFile.getName() + "\n";
 			return (r);
 		}
-		// check input extension
-		ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
-		if (!faFilter.accept(fastaFile)) {
-			r += "(!)Is this a FASTA file? Check extension: " + fastaFile.getName() + "\n";
-		}
 		// set default output filename
 		if (output == null) {
 			String NAME = ExtensionFileFilter.stripExtension(fastaFile) + "_RAND.fa";
 			output = new File(NAME);
 			// check output filename is valid
 		} else {
-			// check ext
-			try {
-				if (!faFilter.accept(output)) {
-					r += "(!)Use FASTA extension for output filename. Try: "
-							+ ExtensionFileFilter.stripExtension(output) + ".fa\n";
-				}
-			} catch (NullPointerException e) {
-				r += "(!)Output filename must have extension: use \".fa\" extension for output filename. Try: " + output
-						+ ".fa\n";
-			}
 			// check directory
 			if (output.getParent() == null) {
 				// System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/cli/Sequence_Analysis/SearchMotifCLI.java b/src/main/java/scriptmanager/cli/Sequence_Analysis/SearchMotifCLI.java
index bb707b77..213c7426 100644
--- a/src/main/java/scriptmanager/cli/Sequence_Analysis/SearchMotifCLI.java
+++ b/src/main/java/scriptmanager/cli/Sequence_Analysis/SearchMotifCLI.java
@@ -75,29 +75,14 @@ private String validateInput() throws IOException {
 			r += "(!)FASTA file does not exist: " + fastaFile.getName() + "\n";
 			return (r);
 		}
-		// check input extensions
-		ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
-		if (!faFilter.accept(fastaFile)) {
-			r += "(!)Is this a FASTA file? Check extension: " + fastaFile.getName() + "\n";
-		}
 		// set default output filename
 		if (output == null) {
 			String NAME = motif + "_" + Integer.toString(ALLOWED_MISMATCH) + "Mismatch_"
 					+ ExtensionFileFilter.stripExtension(fastaFile) + ".bed";
 			NAME += gzOutput ? ".gz" : "";
 			output = new File(NAME);
-			// check output filename is valid
+		// check output filename is valid
 		} else {
-			// check ext
-			try {
-				if (!"bed".equals(ExtensionFileFilter.getExtension(output))) {
-					r += "(!)Use BED extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
-							+ ".bed\n";
-				}
-			} catch (NullPointerException e) {
-				r += "(!)Output filename must have extension: use BED extension for output filename. Try: " + output
-						+ ".bed\n";
-			}
 			// check directory
 			if (output.getParent() == null) {
 // 				System.err.println("default to current directory");
diff --git a/src/main/java/scriptmanager/scripts/BAM_Manipulation/BAMMarkDuplicates.java b/src/main/java/scriptmanager/scripts/BAM_Manipulation/BAMMarkDuplicates.java
index 9d0b25e7..5de200ec 100644
--- a/src/main/java/scriptmanager/scripts/BAM_Manipulation/BAMMarkDuplicates.java
+++ b/src/main/java/scriptmanager/scripts/BAM_Manipulation/BAMMarkDuplicates.java
@@ -6,8 +6,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 
-import javax.swing.JFrame;
-import javax.swing.JOptionPane;
+import htsjdk.samtools.SAMException;
 
 /**
  * Picard wrapper for MarkDuplicates
@@ -15,32 +14,17 @@
  * @author Erik Pavloski
  * @see scriptmanager.window_interface.BAM_Manipulation.BAMMarkDupWindow
  */
-@SuppressWarnings("serial")
-public class BAMMarkDuplicates extends JFrame {
-	File bamFile = null;
-	boolean removeDuplicates = true;
-	File output = null;
-	File metrics = null;
+public class BAMMarkDuplicates {
 	
 	/**
-	 * Creates a new instance of BAMarkDuplicates with a single file
+	 * Runs MarkDuplicates picard tool
 	 * @param in BAM file to be marked
 	 * @param remove Removes duplicates instead of marking them if true
 	 * @param out Output BAM file
 	 * @param met .metrics file for outputting stats
-	 */
-	public BAMMarkDuplicates(File in, boolean remove, File out, File met) {
-		bamFile = in;
-		removeDuplicates = remove;
-		output = out;
-		metrics = met;
-	}
-	
-	/**
-	 * Runs MarkDuplicates picard tool
 	 * @throws IOException Invalid file or parameters If BAM file doesn't have corresponding .BAI Index file
 	 */
-	public void run() throws IOException {
+	public static void mark(File bamFile, boolean removeDuplicates, File output, File metrics) throws IOException {
 		//Check if BAI index file exists
 		File f = new File(bamFile + ".bai");
 		if(f.exists() && !f.isDirectory()) {
@@ -53,7 +37,7 @@ public void run() throws IOException {
             else { args.add("REMOVE_DUPLICATES=false"); }
             markDuplicates.instanceMain(args.toArray(new String[args.size()]));
 		} else {
-			JOptionPane.showMessageDialog(null, "BAI Index File does not exist for: " + bamFile.getName() + "\n");
+			throw new SAMException("BAI Index File does not exist for: " + bamFile.getName() + "\n");
 		}
 	}
 }
\ No newline at end of file
diff --git a/src/main/java/scriptmanager/window_interface/BAM_Manipulation/BAMMarkDupWindow.java b/src/main/java/scriptmanager/window_interface/BAM_Manipulation/BAMMarkDupWindow.java
index 43386b17..73bfc127 100644
--- a/src/main/java/scriptmanager/window_interface/BAM_Manipulation/BAMMarkDupWindow.java
+++ b/src/main/java/scriptmanager/window_interface/BAM_Manipulation/BAMMarkDupWindow.java
@@ -1,5 +1,7 @@
 package scriptmanager.window_interface.BAM_Manipulation;
 
+import htsjdk.samtools.SAMException;
+
 import java.awt.Component;
 import java.awt.Container;
 import java.awt.Color;
@@ -33,8 +35,8 @@
 
 import scriptmanager.objects.LogItem;
 import scriptmanager.util.FileSelection;
-import scriptmanager.cli.BAM_Manipulation.BAMRemoveDupCLI;
 import scriptmanager.scripts.BAM_Manipulation.BAIIndexer;
+import scriptmanager.cli.BAM_Manipulation.BAMRemoveDupCLI;
 import scriptmanager.scripts.BAM_Manipulation.BAMMarkDuplicates;
 
 /**
@@ -78,38 +80,48 @@ class Task extends SwingWorker<Void, Void> {
         @Override
         public Void doInBackground() throws Exception {
         	setProgress(0);
-        	LogItem old_li = null;
-        	for(int x = 0; x < BAMFiles.size(); x++) {
-        		String[] NAME = BAMFiles.get(x).getName().split("\\.");
-        	    File OUTPUT = null;
-        	    File METRICS = null;
-        	    if(OUTPUT_PATH != null) {
-        	    	OUTPUT = new File(OUTPUT_PATH.getCanonicalPath() + File.separator + NAME[0] + "_dedup.bam");
-        	    	METRICS = new File(OUTPUT_PATH.getCanonicalPath() + File.separator + NAME[0] + "_dedup.metrics");
-        	    } else {
-        	    	OUTPUT = new File(NAME[0] + "_dedup.bam");
-        	    	METRICS = new File(NAME[0] + "_dedup.metrics");
-        	    }
-
-				// Initialize LogItem
-        	    String command = BAMRemoveDupCLI.getCLIcommand(BAMFiles.get(x), chckbxRemoveDuplicates.isSelected(), OUTPUT, METRICS);
-				LogItem new_li = new LogItem(command);
-				firePropertyChange("log", old_li, new_li);
-        	    BAMMarkDuplicates dedup = new BAMMarkDuplicates(BAMFiles.get(x), chckbxRemoveDuplicates.isSelected(), OUTPUT, METRICS);
-        	    dedup.run();
+			LogItem old_li = new LogItem("");
+			try {
+				for(int x = 0; x < BAMFiles.size(); x++) {
+					String[] NAME = BAMFiles.get(x).getName().split("\\.");
+					File OUTPUT = null;
+					File METRICS = null;
 
-				// Update log item
-				new_li.setStopTime(new Timestamp(new Date().getTime()));
-				new_li.setStatus(0);
-				old_li = new_li;
+					if(OUTPUT_PATH != null) {
+						OUTPUT = new File(OUTPUT_PATH.getCanonicalPath() + File.separator + NAME[0] + "_dedup.bam");
+						METRICS = new File(OUTPUT_PATH.getCanonicalPath() + File.separator + NAME[0] + "_dedup.metrics");
+					} else {
+						OUTPUT = new File(NAME[0] + "_dedup.bam");
+						METRICS = new File(NAME[0] + "_dedup.metrics");
+					}
+					
 
-        	    if(chckbxGenerateBaiIndex.isSelected()) { BAIIndexer.generateIndex(OUTPUT);	}
+					// Initialize LogItem
+					String command = BAMRemoveDupCLI.getCLIcommand(BAMFiles.get(x), chckbxRemoveDuplicates.isSelected(), OUTPUT, METRICS);
+					LogItem new_li = new LogItem(command);
+					firePropertyChange("log", old_li, new_li);
+					
+					// Run script
+					BAMMarkDuplicates.mark(BAMFiles.get(x), chckbxRemoveDuplicates.isSelected(), OUTPUT, METRICS);
+					
+					// Update log item
+					new_li.setStopTime(new Timestamp(new Date().getTime()));
+					new_li.setStatus(0);
+					old_li = new_li;
+					
+					// Index output if selected
+					if(chckbxGenerateBaiIndex.isSelected()) { BAIIndexer.generateIndex(OUTPUT); }
 
-        	    int percentComplete = (int)(((double)(x + 1) / BAMFiles.size()) * 100);
-        		setProgress(percentComplete);
-        	}
+					// Update progress
+					int percentComplete = (int)(((double)(x + 1) / BAMFiles.size()) * 100);
+					setProgress(percentComplete);
+				}
+			} catch (SAMException se){
+				JOptionPane.showMessageDialog(null, se.getMessage());
+			}
 			firePropertyChange("log", old_li, null);
-        	setProgress(100);
+			setProgress(100);
+
 			JOptionPane.showMessageDialog(null, "Mark Duplicates Complete");
         	return null;
         }
diff --git a/src/main/java/scriptmanager/window_interface/Read_Analysis/TagPileupWindow.java b/src/main/java/scriptmanager/window_interface/Read_Analysis/TagPileupWindow.java
index ebef260b..c36b7b75 100644
--- a/src/main/java/scriptmanager/window_interface/Read_Analysis/TagPileupWindow.java
+++ b/src/main/java/scriptmanager/window_interface/Read_Analysis/TagPileupWindow.java
@@ -124,7 +124,7 @@ public class TagPileupWindow extends JFrame implements ActionListener, PropertyC
 	private CompositeCartoon compositeCartoon;
 
 	// Names of fields indexed by PileupParameters constants
-	private String[] readAspectOptions = {"5' End", "3' End", "Midpoint (Require PE)", "Full Fragment (Require PE)"};
+	private String[] readAspectOptions = {"5' End", "3' End", "Midpoint", "Full Fragment"};
 	private String[] readOutputOptions = {"Read 1", "Read 2", "All Reads"};
 	private String[] transformationOptions = {"None", "Sliding Window", "Gaussian Smooth"};
 
@@ -143,26 +143,28 @@ public Void doInBackground() throws IOException, InterruptedException {
 			try {
 				if (Integer.parseInt(txtBin.getText()) < 1) {
 					JOptionPane.showMessageDialog(null, "Invalid Bin Size!!! Must be larger than 0 bp");
+				} else if (Integer.parseInt(txtTagExtend.getText()) < 0) {
+					JOptionPane.showMessageDialog(null, "Invalid Tag Extend length!!! Must be non-negative bp length" + "\n\n" + "Consider adjusting the shift bp value if you are interested in negative extensions.", "Validate Input", JOptionPane.ERROR_MESSAGE);
 				} else if (cbox_Transform.getSelectedIndex()==PileupParameters.WINDOW && Integer.parseInt(txtSmooth.getText()) < 1) {
-					JOptionPane.showMessageDialog(null, "Invalid Smoothing Window Size!!! Must be larger than 0 bp");
+					JOptionPane.showMessageDialog(null, "Invalid Smoothing Window Size!!! Must be larger than 0 bp", "Validate Input", JOptionPane.ERROR_MESSAGE);
 				} else if (cbox_Transform.getSelectedIndex()==PileupParameters.WINDOW && Integer.parseInt(txtSmooth.getText()) % 2 == 0) {
-					JOptionPane.showMessageDialog(null, "Invalid Smoothing Window Size!!! Must be odd for symmetrical smoothing (so that the window is centered properly).");
+					JOptionPane.showMessageDialog(null, "Invalid Smoothing Window Size!!! Must be odd for symmetrical smoothing (so that the window is centered properly).", "Validate Options", JOptionPane.ERROR_MESSAGE);
 				} else if (cbox_Transform.getSelectedIndex()==PileupParameters.GAUSSIAN && Integer.parseInt(txtStdSize.getText()) < 1) {
-					JOptionPane.showMessageDialog(null, "Invalid Standard Deviation Size!!! Must be larger than 0 bp");
+					JOptionPane.showMessageDialog(null, "Invalid Standard Deviation Size!!! Must be larger than 0 bp", "Validate Input", JOptionPane.ERROR_MESSAGE);
 				} else if (cbox_Transform.getSelectedIndex()==PileupParameters.GAUSSIAN && Integer.parseInt(txtNumStd.getText()) < 1) {
-					JOptionPane.showMessageDialog(null, "Invalid Number of Standard Deviations!!! Must be larger than 0");
+					JOptionPane.showMessageDialog(null, "Invalid Number of Standard Deviations!!! Must be larger than 0", "Validate Input", JOptionPane.ERROR_MESSAGE);
 				} else if (Integer.parseInt(txtCPU.getText()) < 1) {
-					JOptionPane.showMessageDialog(null, "Invalid Number of CPU's!!! Must use at least 1");
+					JOptionPane.showMessageDialog(null, "Invalid Number of CPU's!!! Must use at least 1", "Validate Input", JOptionPane.ERROR_MESSAGE);
 				} else if (chckbxFilterByMin.isSelected() && Integer.parseInt(txtMin.getText()) < 0) {
-					JOptionPane.showMessageDialog(null, "Invalid Minimum Insert Size!!! Must be greater than or equal to 0 bp");
+					JOptionPane.showMessageDialog(null, "Invalid Minimum Insert Size!!! Must be greater than or equal to 0 bp", "Validate Input", JOptionPane.ERROR_MESSAGE);
 				} else if (chckbxFilterByMax.isSelected() && Integer.parseInt(txtMax.getText()) < 0) {
-					JOptionPane.showMessageDialog(null, "Invalid Maximum Insert Size!!! Must be greater than or equal to 0 bp");
+					JOptionPane.showMessageDialog(null, "Invalid Maximum Insert Size!!! Must be greater than or equal to 0 bp", "Validate Input", JOptionPane.ERROR_MESSAGE);
 				} else if (chckbxFilterByMin.isSelected() && chckbxFilterByMax.isSelected() && Integer.parseInt(txtMax.getText()) < Integer.parseInt(txtMin.getText())) {
-					JOptionPane.showMessageDialog(null, "Invalid Maximum & Minimum Insert Sizes!!! Maximum must be larger/equal to Minimum!");
+					JOptionPane.showMessageDialog(null, "Invalid Maximum & Minimum Insert Sizes!!! Maximum must be larger/equal to Minimum!", "Validate Input", JOptionPane.ERROR_MESSAGE);
 				} else if (BEDFiles.size() < 1) {
-					JOptionPane.showMessageDialog(null, "No BED Files Loaded!!!");
+					JOptionPane.showMessageDialog(null, "No BED Files Loaded!!!", "Validate Input", JOptionPane.ERROR_MESSAGE);
 				} else if (BAMFiles.size() < 1) {
-					JOptionPane.showMessageDialog(null, "No BAM Files Loaded!!!");
+					JOptionPane.showMessageDialog(null, "No BAM Files Loaded!!!", "Validate Input", JOptionPane.ERROR_MESSAGE);
 				} else {
 					setProgress(0);
 					// Load up parameters for the pileup into single object
@@ -250,9 +252,9 @@ public void propertyChange(PropertyChangeEvent evt) {
 					return null;
 				}
 			} catch (NumberFormatException nfe) {
-				JOptionPane.showMessageDialog(null, "Invalid Input in Fields!!!");
+				JOptionPane.showMessageDialog(null, "Invalid Input in Fields!!!", "Validate Input", JOptionPane.ERROR_MESSAGE);
 			} catch (SAMException se) {
-				JOptionPane.showMessageDialog(null, se.getMessage());
+				JOptionPane.showMessageDialog(null, se.getMessage(), "Validate Input", JOptionPane.ERROR_MESSAGE);
 			}
 			return null;
 		}
@@ -565,7 +567,7 @@ public void itemStateChanged(ItemEvent e) {
 		sl_ReadManipulation.putConstraint(SpringLayout.NORTH, txtTagExtend, -1, SpringLayout.NORTH, lblTagExtend);
 		sl_ReadManipulation.putConstraint(SpringLayout.WEST, txtTagExtend, 120, SpringLayout.WEST, lblTagExtend);
 		sl_ReadManipulation.putConstraint(SpringLayout.EAST, txtTagExtend, -6, SpringLayout.EAST, pnlReadManipulation);
-		txtTagExtend.setText("1");
+		txtTagExtend.setText("0");
 		txtTagExtend.setHorizontalAlignment(SwingConstants.CENTER);
 		txtTagExtend.setColumns(10);
 		pnlReadManipulation.add(txtTagExtend);