From c663c88093e00cd91fe7327f4dccad10f51058ce Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 10 Feb 2020 11:12:30 +0100
Subject: [PATCH] SCHWED-4382: Better logging for HHblits

---
 modules/bindings/pymod/hhblits.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 5567dd229..ff08319a4 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -624,8 +624,17 @@ class HHblits:
             return hhm_file
         ost.LogVerbose('converting %s to %s' % (a3m_file, hhm_file))
         os.putenv('HHLIB', self.hhlib_dir)
-        if subprocess.call('%s -i %s -o %s' % (hhmake, a3m_file, hhm_file),
-                           shell=True):
+        job = subprocess.Popen('%s -i %s -o %s' % (hhmake, a3m_file, hhm_file),
+                               shell=True, stdout=subprocess.PIPE,
+                               stderr=subprocess.PIPE)
+        sout, serr = job.communicate()
+        lines = serr.decode().splitlines()
+        for line in lines:
+            ost.LogWarning(line)
+        lines = sout.decode().splitlines()
+        for line in lines:
+            ost.LogVerbose(line)
+        if job.returncode !=0:
             raise IOError('could not convert a3m to hhm file')
         return hhm_file
 
-- 
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