diff --git a/src/edu/msu/cme/rdp/classifier/ClassifierCmd.java b/src/edu/msu/cme/rdp/classifier/ClassifierCmd.java
index 366e96f..20f0cdb 100644
--- a/src/edu/msu/cme/rdp/classifier/ClassifierCmd.java
+++ b/src/edu/msu/cme/rdp/classifier/ClassifierCmd.java
@@ -68,7 +68,7 @@ public void doClassify(String inputFile, String outFile, String propfile, Classi
                     wt.write(ClassificationResultFormatter.getOutput(result, format));
 
                 } catch (ShortSequenceException e) {
-                    System.out.println(e.getMessage());
+                    System.err.println(e.getMessage());
                 } catch (Exception e) {
                     e.printStackTrace();
                 }
@@ -181,7 +181,7 @@ public static void main(String[] args) throws Exception {
             queryFile = args[0];
             
         } catch (Exception e) {
-            System.out.println("Command Error: " + e.getMessage());
+            System.err.println("Command Error: " + e.getMessage());
             new HelpFormatter().printHelp(120, "ClassifierCmd [options] <samplefile>\nNote this is the legacy command for one sample classification ", "", options, "");
 
             return;
diff --git a/src/edu/msu/cme/rdp/classifier/comparison/ComparisonCmd.java b/src/edu/msu/cme/rdp/classifier/comparison/ComparisonCmd.java
index 7db37f0..3a59419 100644
--- a/src/edu/msu/cme/rdp/classifier/comparison/ComparisonCmd.java
+++ b/src/edu/msu/cme/rdp/classifier/comparison/ComparisonCmd.java
@@ -97,7 +97,7 @@ public void doClassify(String s1, String s2, String detailFile, String sigFile,
                     wt.write(ClassificationResultFormatter.getOutput(result, format));
 
                 } catch (ShortSequenceException e) {
-                    System.out.println(e.getMessage());
+                    System.err.println(e.getMessage());
                 } catch (Exception e) {
                     e.printStackTrace();
                 }
@@ -111,7 +111,7 @@ public void doClassify(String s1, String s2, String detailFile, String sigFile,
                     wt.write(ClassificationResultFormatter.getOutput(result, format));
 
                 } catch (ShortSequenceException e) {
-                    System.out.println(e.getMessage());
+                    System.err.println(e.getMessage());
                 } catch (Exception e) {
                     e.printStackTrace();
                 }
@@ -301,7 +301,7 @@ public static void main(String[] args) throws Exception {
                 }
             }
         } catch (Exception e) {
-            System.out.println("Command Error: " + e.getMessage());
+            System.err.println("Command Error: " + e.getMessage());
             new HelpFormatter().printHelp(120, "ComparisonCmd", "", options, "", true);
             return;
         }
@@ -318,4 +318,4 @@ public static void main(String[] args) throws Exception {
         cmd.doClassify(queryFile1, queryFile2, class_outputFile, compare_outputFile, format);
 
     }
-}
\ No newline at end of file
+}
diff --git a/src/edu/msu/cme/rdp/classifier/train/ClassifierTraineeMaker.java b/src/edu/msu/cme/rdp/classifier/train/ClassifierTraineeMaker.java
index 37e7d18..dcd2b8f 100644
--- a/src/edu/msu/cme/rdp/classifier/train/ClassifierTraineeMaker.java
+++ b/src/edu/msu/cme/rdp/classifier/train/ClassifierTraineeMaker.java
@@ -162,7 +162,7 @@ public static void main(String[] args) throws FileNotFoundException,
             }
             
         } catch (Exception e) {
-            System.out.println("Command Error: " + e.getMessage());
+            System.err.println("Command Error: " + e.getMessage());
             new HelpFormatter().printHelp(120, "train", "", options, "", true);
             return;
         }
diff --git a/src/edu/msu/cme/rdp/classifier/train/LineageSequenceParser.java b/src/edu/msu/cme/rdp/classifier/train/LineageSequenceParser.java
index f0d9fb1..36d7f1e 100644
--- a/src/edu/msu/cme/rdp/classifier/train/LineageSequenceParser.java
+++ b/src/edu/msu/cme/rdp/classifier/train/LineageSequenceParser.java
@@ -128,7 +128,7 @@ private String modifySequence(String s) {
             out.close();
             return out.toString();
         } catch (IOException e) {
-            System.out.println("In StringReader or StringWriter exception : " + e.getMessage());
+            System.err.println("In StringReader or StringWriter exception : " + e.getMessage());
         }
         return null;
     }
diff --git a/src/edu/msu/cme/rdp/classifier/train/validation/leaveoneout/LeaveOneOutTesterMain.java b/src/edu/msu/cme/rdp/classifier/train/validation/leaveoneout/LeaveOneOutTesterMain.java
index 9d56c37..3a0dde6 100644
--- a/src/edu/msu/cme/rdp/classifier/train/validation/leaveoneout/LeaveOneOutTesterMain.java
+++ b/src/edu/msu/cme/rdp/classifier/train/validation/leaveoneout/LeaveOneOutTesterMain.java
@@ -177,7 +177,7 @@ public static void main(String[] args) throws FileNotFoundException, IOException
                 GoodWordIterator.setWordSize(kmer);
             }*/
         } catch (Exception e) {
-            System.out.println("Command Error: " + e.getMessage());
+            System.err.println("Command Error: " + e.getMessage());
             new HelpFormatter().printHelp(120, "LeaveOneOutTesterMain", "", options, "", true);
             return;
         }
diff --git a/src/edu/msu/cme/rdp/classifier/utils/HierarchyVersion.java b/src/edu/msu/cme/rdp/classifier/utils/HierarchyVersion.java
index 74b8ba8..d1c9451 100644
--- a/src/edu/msu/cme/rdp/classifier/utils/HierarchyVersion.java
+++ b/src/edu/msu/cme/rdp/classifier/utils/HierarchyVersion.java
@@ -26,7 +26,7 @@ public class HierarchyVersion {
   	 try{
         versionPattern = Pattern.compile(regex);
       } catch(PatternSyntaxException pse){
-        System.out.println("There is a problem with the regular expression! " + regex);
+        System.err.println("There is a problem with the regular expression! " + regex);
       }
   }
   
diff --git a/src/edu/msu/cme/rdp/multicompare/Main.java b/src/edu/msu/cme/rdp/multicompare/Main.java
index b69f4b4..27c515c 100644
--- a/src/edu/msu/cme/rdp/multicompare/Main.java
+++ b/src/edu/msu/cme/rdp/multicompare/Main.java
@@ -239,7 +239,7 @@ public static void main(String[] args) throws Exception {
                 throw new IllegalArgumentException("Require at least one sample files");
             }
         }catch (Exception e) {
-            System.out.println("Command Error: " + e.getMessage());
+            System.err.println("Command Error: " + e.getMessage());
             new HelpFormatter().printHelp(80, " [options] <samplefile>[,idmappingfile] ...", "", options, "");
             return;
         }
diff --git a/src/edu/msu/cme/rdp/multicompare/Reprocess.java b/src/edu/msu/cme/rdp/multicompare/Reprocess.java
index 06eaa16..60a37ce 100644
--- a/src/edu/msu/cme/rdp/multicompare/Reprocess.java
+++ b/src/edu/msu/cme/rdp/multicompare/Reprocess.java
@@ -169,7 +169,7 @@ public static void main(String [] args) throws Exception {
               
             }
         } catch (Exception e) {
-            System.out.println("Command Error: " + e.getMessage());
+            System.err.println("Command Error: " + e.getMessage());
             new HelpFormatter().printHelp(120, "Reprocess [options] <Classification_allrank_result>[,idmappingfile] ...", "", options, "");
             return;
         }