diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
index 926afe1..c8cfe6d 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h4/MergePathsH4.java
@@ -364,9 +364,15 @@
         RunningJob job = JobClient.runJob(conf);
         
         // move the tmp outputs to the arg-spec'ed dirs
-        dfs.rename(new Path(outputPath + File.pathSeparator +  MergePathsH4Reducer.TO_MERGE_OUTPUT), new Path(toMergeOutput));
-        dfs.rename(new Path(outputPath + File.pathSeparator +  MergePathsH4Reducer.COMPLETE_OUTPUT), new Path(completeOutput));
-        dfs.rename(new Path(outputPath + File.pathSeparator +  MergePathsH4Reducer.UPDATES_OUTPUT), new Path(updatesOutput));
+        if (!dfs.rename(new Path(outputPath + File.separator +  MergePathsH4Reducer.TO_MERGE_OUTPUT), new Path(toMergeOutput))) {
+            dfs.mkdirs(new Path(toMergeOutput));
+        }
+        if (!dfs.rename(new Path(outputPath + File.separator +  MergePathsH4Reducer.COMPLETE_OUTPUT), new Path(completeOutput))) {
+            dfs.mkdirs(new Path(completeOutput));
+        }
+        if (!dfs.rename(new Path(outputPath + File.separator +  MergePathsH4Reducer.UPDATES_OUTPUT), new Path(updatesOutput))) {
+            dfs.mkdirs(new Path(updatesOutput));
+        }
         
         return job;
     }
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java
index 2974d4c..71d2295 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java
@@ -240,7 +240,7 @@
         conf.setJobName("PathNodeInitial " + inputPath);
 
         FileInputFormat.addInputPaths(conf, inputPath);
-        Path outputPath = new Path(inputPath + ".initialMerge.tmp");
+        Path outputPath = new Path(inputPath.replaceAll("/$",  "") + ".initialMerge.tmp");
         FileOutputFormat.setOutputPath(conf, outputPath);
 
         conf.setInputFormat(SequenceFileInputFormat.class);
@@ -264,8 +264,8 @@
         RunningJob job = JobClient.runJob(conf);
         
         // move the tmp outputs to the arg-spec'ed dirs
-        dfs.rename(new Path(outputPath + File.pathSeparator +  TO_MERGE_OUTPUT), new Path(toMergeOutput));
-        dfs.rename(new Path(outputPath + File.pathSeparator +  COMPLETE_OUTPUT), new Path(completeOutput));
+        dfs.rename(new Path(outputPath + File.separator +  TO_MERGE_OUTPUT), new Path(toMergeOutput));
+        dfs.rename(new Path(outputPath + File.separator +  COMPLETE_OUTPUT), new Path(completeOutput));
         
         return job;
     }