From eb045df2490c1f096e0752f16fc58c7b996c0406 Mon Sep 17 00:00:00 2001
From: Michael Nuhn <mnuhn@ebi.ac.uk>
Date: Thu, 28 Jan 2016 11:17:48 +0000
Subject: [PATCH] Avoid potential 'Inappropriate ioctl for device' errors when
 ccat tries to write to stderr

---
 modules/Bio/EnsEMBL/Funcgen/Sequencing/PeakCaller/CCAT.pm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Funcgen/Sequencing/PeakCaller/CCAT.pm b/modules/Bio/EnsEMBL/Funcgen/Sequencing/PeakCaller/CCAT.pm
index 057875c79..e4d1eb4d0 100644
--- a/modules/Bio/EnsEMBL/Funcgen/Sequencing/PeakCaller/CCAT.pm
+++ b/modules/Bio/EnsEMBL/Funcgen/Sequencing/PeakCaller/CCAT.pm
@@ -134,7 +134,10 @@ sub run {
                       $conf_file,
                       $out_prefix,
                       '>',
-                      $out_prefix.'.log');
+                      $out_prefix.'.log',
+                      '2>',
+                      $out_prefix.'.stderr.log'
+                      );
   #WARNING!
   #Do not remove this redirect to log file, as th CCAT binary will expect that 
   #it is directly attached to a terminal and fails with: