From 56da6343af1faee8d9919d412fbe57b349d86b38 Mon Sep 17 00:00:00 2001
From: Sina Majidian <sina.majidian@gmail.com>
Date: Sat, 30 Mar 2024 17:35:52 +0100
Subject: [PATCH] improve logging Mapper.py

---
 read2tree/Mapper.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/read2tree/Mapper.py b/read2tree/Mapper.py
index 93481834..f46baff3 100644
--- a/read2tree/Mapper.py
+++ b/read2tree/Mapper.py
@@ -629,15 +629,18 @@ def _output_shell(self, line):
         :return:
         """
         try:
+            self.logger.debug("Running " + line)
             shell_command = subprocess.Popen(
                 line, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
                 shell=True)
-        except OSError:
-            return None
-        except ValueError:
+        except:
+            self.logger.debug("Shell command failed to execute by running ")
             return None
 
         (output, err) = shell_command.communicate()
+        self.logger.debug("Shell output: "+ str(output))
+        self.logger.debug("Shell err: " + str(err))
+        
         shell_command.wait()
         if shell_command.returncode != 0:
             self.logger.debug("Shell command failed to execute")