diff --git a/CMakeLists.txt b/CMakeLists.txt
index 52fb339..8f1d104 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,10 +4,10 @@ enable_testing()
 
 project (Sailfish)
 
-set(CPACK_PACKAGE_VERSION "0.6.1")
+set(CPACK_PACKAGE_VERSION "0.6.2")
 set(CPACK_PACKAGE_VERSION_MAJOR "0")
 set(CPACK_PACKAGE_VERSION_MINOR "6")
-set(CPACK_PACKAGE_VERSION_PATCH "1")
+set(CPACK_PACKAGE_VERSION_PATCH "2")
 set(CPACK_GENERATOR "TGZ")
 set(CPACK_SOURCE_GENERATOR "TGZ")
 set(CPACK_PACKAGE_VENDOR "Carnegie Mellon University")
diff --git a/include/SailfishConfig.hpp b/include/SailfishConfig.hpp
index 24ee037..fedaeda 100644
--- a/include/SailfishConfig.hpp
+++ b/include/SailfishConfig.hpp
@@ -28,8 +28,8 @@
 namespace Sailfish {
 	constexpr char majorVersion[] = "0";
 	constexpr char minorVersion[] = "6";
-	constexpr char patchVersion[] = "1";
-	constexpr char version[] = "0.6.1";
+	constexpr char patchVersion[] = "2";
+	constexpr char version[] = "0.6.2";
 }
 
 #endif // SAILFISH_CONFIG_HPP
diff --git a/src/IndexedCounter.cpp b/src/IndexedCounter.cpp
index 28d850a..73de2c1 100644
--- a/src/IndexedCounter.cpp
+++ b/src/IndexedCounter.cpp
@@ -166,7 +166,7 @@ bool countKmers(ParserT& parser, PerfectHashIndex& phi, CountDBNew& rhash, size_
                             switch(c) {
                                 case jellyfish::CODE_IGNORE: break;
                                 case jellyfish::CODE_COMMENT:
-                                  std::cerr << "ERROR\n";
+                                    std::cerr << "ERROR: unexpected character " << c << " in read!\n";
 
                                 // Fall through
                                 case jellyfish::CODE_RESET:
@@ -318,8 +318,8 @@ int mainCount( int argc, char *argv[] ) {
     ("help,h", "produce help message")
     ("index,i", po::value<string>(), "transcript index file [Sailfish format]")
     ("reads,r", po::value<std::vector<string>>(&undirReadFiles)->multitoken(), "List of files containing \"undirected\" reads")
-    ("reverse,R", po::value<std::vector<string>>(&fwdReadFiles)->multitoken(), "List of files containing \"sense\" reads")
-    ("forward,F", po::value<std::vector<string>>(&revReadFiles)->multitoken(), "List of files containing \"anti-sense\" reads")
+    ("reverse,R", po::value<std::vector<string>>(&revReadFiles)->multitoken(), "List of files containing \"anti-sense\" reads")
+    ("forward,F", po::value<std::vector<string>>(&fwdReadFiles)->multitoken(), "List of files containing \"sense\" reads")
     ("counts,c", po::value<string>(), "File where Sailfish read count is written")
     ("threads,p", po::value<uint32_t>()->default_value(maxThreads), "The number of threads to use when counting kmers")
     ("polya,a", po::bool_switch(), "polyA/polyT k-mers should be discarded")
diff --git a/src/QuantificationDriver.cpp b/src/QuantificationDriver.cpp
index 1121b76..f829093 100644
--- a/src/QuantificationDriver.cpp
+++ b/src/QuantificationDriver.cpp
@@ -61,27 +61,38 @@ int runKmerCounter(const std::string& sfCommand,
     argStream << "--counts " << countFileOut << " ";
     argStream << "--threads " << numThreads << " ";
 
+    std::cerr << "Undirected reads:[";
     // Undirected reads
-    argStream << "--reads ";
-    for (auto& rfile : undirReadFiles) {
-        argStream << rfile << " ";
+    if (undirReadFiles.size() > 0) {
+        argStream << "--reads=";
+        for (auto& rfile : undirReadFiles) {
+            std::cerr << rfile << " ";
+            argStream << rfile << " ";
+        }
     }
+    std::cerr << "]\n";
 
+    std::cerr << "Sense reads:[";
     // Sense reads
     if (fwdReadFiles.size() > 0) {
-      argStream << "--forward";
+      argStream << "--forward=";
       for (auto& rfile : fwdReadFiles) {
-        argStream << rfile << " ";
+          std::cerr << rfile << " ";
+          argStream << rfile << " ";
       }
     }
+    std::cerr << "]\n";
 
+    std::cerr << "Anti-sense reads:[";
     // Anti-sense reads
     if (revReadFiles.size() > 0) {
-      argStream << "--reverse";
+      argStream << "--reverse=";
       for (auto& rfile : revReadFiles) {
-        argStream << rfile << " ";
+          std::cerr << rfile << " ";
+          argStream << rfile << " ";
       }
     }
+    std::cerr << "]\n";
 
     std::string argString = argStream.str();
     boost::trim(argString);