diff --git a/src/main/java/picard/analysis/CollectBaseDistributionByCycle.java b/src/main/java/picard/analysis/CollectBaseDistributionByCycle.java
index 1dc127d80b..db2f0a3e42 100644
--- a/src/main/java/picard/analysis/CollectBaseDistributionByCycle.java
+++ b/src/main/java/picard/analysis/CollectBaseDistributionByCycle.java
@@ -137,7 +137,10 @@ protected void finish() {
         metrics.write(OUTPUT);
         if (hist.isEmpty()) {
             log.warn("No valid bases found in input file. No plot will be produced.");
-        } else {
+            return;
+        }
+
+        if (CHART_OUTPUT != null) {
             final int rResult = RExecutor.executeFromClasspath("picard/analysis/baseDistributionByCycle.R",
                     OUTPUT.getAbsolutePath(),
                     CHART_OUTPUT.getAbsolutePath().replaceAll("%", "%%"),
diff --git a/src/main/java/picard/analysis/CollectGcBiasMetrics.java b/src/main/java/picard/analysis/CollectGcBiasMetrics.java
index 21def4cc81..a03438ee0a 100644
--- a/src/main/java/picard/analysis/CollectGcBiasMetrics.java
+++ b/src/main/java/picard/analysis/CollectGcBiasMetrics.java
@@ -206,13 +206,15 @@ private void writeResultsToFiles() {
         detailMetricsFile.write(OUTPUT);
         summaryMetricsFile.write(SUMMARY_OUTPUT);
 
-        final NumberFormat fmt = NumberFormat.getIntegerInstance();
-        fmt.setGroupingUsed(true);
-        RExecutor.executeFromClasspath(R_SCRIPT,
-                OUTPUT.getAbsolutePath(),
-                SUMMARY_OUTPUT.getAbsolutePath(),
-                CHART_OUTPUT.getAbsolutePath().replaceAll("%", "%%"),
-                String.valueOf(SCAN_WINDOW_SIZE));
+        if (CHART_OUTPUT != null) {
+            final NumberFormat fmt = NumberFormat.getIntegerInstance();
+            fmt.setGroupingUsed(true);
+            RExecutor.executeFromClasspath(R_SCRIPT,
+                    OUTPUT.getAbsolutePath(),
+                    SUMMARY_OUTPUT.getAbsolutePath(),
+                    CHART_OUTPUT.getAbsolutePath().replaceAll("%", "%%"),
+                    String.valueOf(SCAN_WINDOW_SIZE));
+        }
     }
 }
 
diff --git a/src/main/java/picard/analysis/CollectInsertSizeMetrics.java b/src/main/java/picard/analysis/CollectInsertSizeMetrics.java
index d6d7916a8a..9f40458db5 100644
--- a/src/main/java/picard/analysis/CollectInsertSizeMetrics.java
+++ b/src/main/java/picard/analysis/CollectInsertSizeMetrics.java
@@ -167,10 +167,12 @@ protected String[] customCommandLineValidation() {
                      " of the total aligned paired data.");
             final InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector allReadsCollector = (InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector) multiCollector.getAllReadsCollector();
             log.warn("Total mapped pairs in all categories: " + (allReadsCollector == null ? allReadsCollector : allReadsCollector.getTotalInserts()));
+            return;
         }
-        else  {
-            file.write(OUTPUT);
 
+        file.write(OUTPUT);
+
+        if (Histogram_FILE != null) {
             final List<String> plotArgs = new ArrayList<>();
             Collections.addAll(plotArgs, OUTPUT.getAbsolutePath(), Histogram_FILE.getAbsolutePath().replaceAll("%", "%%"), INPUT.getName());
 
diff --git a/src/main/java/picard/analysis/MeanQualityByCycle.java b/src/main/java/picard/analysis/MeanQualityByCycle.java
index 81891b1390..40b74e63a1 100644
--- a/src/main/java/picard/analysis/MeanQualityByCycle.java
+++ b/src/main/java/picard/analysis/MeanQualityByCycle.java
@@ -135,8 +135,10 @@ protected void finish() {
 
         if (q.isEmpty() && oq.isEmpty()) {
             log.warn("No valid bases found in input file. No plot will be produced.");
+            return;
         }
-        else {
+
+        if(CHART_OUTPUT != null) {
             // Now run R to generate a chart
             final int rResult = RExecutor.executeFromClasspath(
                     "picard/analysis/meanQualityByCycle.R",
diff --git a/src/main/java/picard/analysis/QualityScoreDistribution.java b/src/main/java/picard/analysis/QualityScoreDistribution.java
index db867ad18c..216c159a5e 100644
--- a/src/main/java/picard/analysis/QualityScoreDistribution.java
+++ b/src/main/java/picard/analysis/QualityScoreDistribution.java
@@ -158,8 +158,10 @@ protected void finish() {
         metrics.write(OUTPUT);
         if (qHisto.isEmpty() && oqHisto.isEmpty()) {
             log.warn("No valid bases found in input file. No plot will be produced.");
+            return;
         }
-        else {
+
+        if (CHART_OUTPUT != null) {
             // Now run R to generate a chart
             final int rResult = RExecutor.executeFromClasspath(
                     "picard/analysis/qualityScoreDistribution.R",