diff --git a/pipeline/check/quality.py b/pipeline/check/quality.py
index 2cc70e0..0b8c6c6 100644
--- a/pipeline/check/quality.py
+++ b/pipeline/check/quality.py
@@ -45,8 +45,9 @@ def check_hisat2(filename, cutoff=0, log=None):
 
     with open(filename, 'r') as f:
         lines = '\t'.join(f.readlines())
-        print(lines)
         for l in lines:
+            l = l.strip()
+            print(l)
             if "overall alignment" in l:
                 hits = re_mapped.search(l)
                 print(hits)