From 90809ed28ac6d07f20f533f8a0108d3557cc1bc4 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 11 Mar 2026 14:38:28 -0500
Subject: Check whether files exist before attempting to operate on them.

---
 scripts/run_qtlreaper.py | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/scripts/run_qtlreaper.py b/scripts/run_qtlreaper.py
index a0c3b22..d9cadea 100644
--- a/scripts/run_qtlreaper.py
+++ b/scripts/run_qtlreaper.py
@@ -160,16 +160,20 @@ def dispatch(args: Namespace) -> int:
                 while _qtlreaper.poll() is None:
                     logger.debug("QTLReaper process running…")
                     time.sleep(1)
-                    results = tuple(#type: ignore[var-annotated]
-                        max(qtls, key=lambda qtl: qtl["LRS"])
-                        for qtls in
-                        reduce(__qtls_by_trait__,
-                               parse_tsv_file(_qtlreaper_main_output),
-                               {}).values())
-            save_qtl_values_to_db(conn, results)
+                    results = (
+                        tuple(#type: ignore[var-annotated]
+                            max(qtls, key=lambda qtl: qtl["LRS"])
+                            for qtls in
+                            reduce(__qtls_by_trait__,
+                                   parse_tsv_file(_qtlreaper_main_output),
+                                   {}).values())
+                        if _qtlreaper_main_output.exists()
+                        else tuple())
             logger.debug("Cleaning up temporary files.")
-            _traitsfile.unlink()
-            _qtlreaper_main_output.unlink()
+
+            # short-circuits to delete file if exists
+            _traitsfile.exists() and _traitsfile.unlink()
+            _qtlreaper_main_output.exists() and _qtlreaper_main_output.unlink()
             logger.info("Successfully computed p values for %s traits.", len(_traitsdata))
             return 0
         except FileNotFoundError as fnf:
-- 
cgit 1.4.1