Cleaner stderr prints

python/obitools3/commands/alignpairedend.pyx

@@ -226,6 +226,9 @@ def run(config):
     
         i+=1
 
+    pb(i, force=True)
+    print("", file=sys.stderr)
+
     if kmer_ali :
         aligner.free()
 
@@ -234,11 +237,13 @@ def run(config):
     view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
     output[0].record_command_line(command_line)
 
-    print("\n")
-    print(repr(view))
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(view), file=sys.stderr)
     
     input[0].close()
     if two_views:
         rinput[0].close()
     output[0].close()
 
+    logger("info", "Done.")
+