hide all warning/technical output from user

backend/main.py

@@ -103,18 +103,15 @@ async def run_bootstrap(job_id, model_paths, mapping_paths, expr_path, species_p
         await loop.run_in_executor(None, run_sync)
         job["progress"] = 80
 
-        # Relay captured stdout as messages
+        # Relay only key status lines — skip all Warning lines
         for line in captured.getvalue().strip().split("\n"):
             line = line.strip()
-            if not line:
+            if not line or line.startswith("Warning"):
                 continue
             if "Write to" in line:
-                type_ = "ok"
-            elif line.startswith("Warning"):
-                type_ = ""   # warnings are noisy — show but no colour
-            else:
-                type_ = "info"
-            add_msg(line, type_)
+                add_msg("Writing output files…", "ok")
+            elif line.startswith("Read") or line.startswith("Species") or line.startswith("Bootstrap"):
+                add_msg(line, "info")
 
         add_msg("Compressing output files…", "info")
         job["progress"] = 90

frontend/index.html

@@ -748,7 +748,13 @@ async function startJob() {
     if (d.progress !== undefined) {
       document.getElementById('progressBar').style.width = d.progress + '%';
       document.getElementById('progressPct').textContent = d.progress + '%';
-      if (d.label) document.getElementById('progressLabel').textContent = d.label;
+      // Show only clean status labels, never raw backend output
+      const cleanLabels = ['Starting…', 'Files received. Starting bootstrap…', 'Writing output files…', 'Compressing output files…', 'Processing…'];
+      if (d.label && cleanLabels.some(l => d.label.startsWith(l.split('…')[0]))) {
+        document.getElementById('progressLabel').textContent = d.label;
+      } else if (d.progress > 0 && d.progress < 100) {
+        document.getElementById('progressLabel').textContent = 'Processing…';
+      }
     }
 
     if (d.status === 'done') {