diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java
index cb92bd051..20819c231 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java
@@ -141,7 +141,7 @@ else if (header.getReadGroups().size() > 1)
 
                     String rgId = header.getReadGroups().get(0).getSample();
 
-                    JSONObject json = new JSONObject(FileUtils.readFileToString(coverageFile, Charset.defaultCharset()));
+                    JSONObject json = new JSONObject(FileUtils.readFileToString(coverageJson, Charset.defaultCharset()));
                     writer.println("id\tpath\tdepth\tread length");
                     double depth = json.getJSONObject("autosome").getDouble("depth");
                     double readLength = json.getInt("read_length");