diff --git a/CMake/mlpack_coverage.in b/CMake/mlpack_coverage.in
index 6dc2204294..6351b1232c 100755
--- a/CMake/mlpack_coverage.in
+++ b/CMake/mlpack_coverage.in
@@ -92,6 +92,8 @@ else
 fi
 
 echo "Filtering coverage files..."
+# Clear negative entries in coverage file
+sed -E 's/-([0-9]+)/50000/g' -i .coverage.wtest.run
 # Merge coverage tracefiles.
 lcov -a .coverage.wtest.base -a .coverage.wtest.run  -o .coverage.total >> ./coveragehistory/$current_log_file