diff --git a/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java b/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java
index 8ae669225..9ace8204e 100644
--- a/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java
+++ b/MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java
@@ -272,6 +272,10 @@ private static void runSkyline(String skylinePath, Path wd, String skylineVersio
       Process skylineProcess = null;
       try {
         System.out.println("Running command: " + String.join(" ", cmd));
+
+        System.out.println("Content of " + pp.toAbsolutePath() + ":");
+        System.out.println(new String(Files.readAllBytes(pp)));
+
         ProcessBuilder pb = new ProcessBuilder(cmd);
         ProcessBuilderInfo pbi = new PbiBuilder().setPb(pb).setName(pb.toString()).setFnStdOut(null).setFnStdErr(null).setParallelGroup(null).create();
         ProcessResult pr = new ProcessResult(pbi);