From d74b77be7d6b8167c8ed1769a39a38d495f93760 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 8 Oct 2020 12:10:34 +0200
Subject: [PATCH] Write errors with prokka to correct logger
---
PanACoTA/annotate_module/annotation_functions.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/PanACoTA/annotate_module/annotation_functions.py b/PanACoTA/annotate_module/annotation_functions.py
index 3a4dc9c5..523147ba 100755
--- a/PanACoTA/annotate_module/annotation_functions.py
+++ b/PanACoTA/annotate_module/annotation_functions.py
@@ -262,7 +262,7 @@ def run_prokka(arguments):
error = (f"Error while trying to run prokka on {name} from {gpath}")
logger.details("Prokka command: " + cmd)
prokf = open(prok_logfile, "w")
- ret = utils.run_cmd(cmd, error, eof=False, stderr=prokf)
+ ret = utils.run_cmd(cmd, error, eof=False, stderr=prokf, logger=logger)
prokf.close()
if ret.returncode != 0:
return False
--
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