From b5f5b9de9ef059266399567d002c92406a96d139 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 29 Apr 2021 21:28:59 +0200
Subject: [PATCH] correctly log accpro errors
---
docker/run_qmean.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/docker/run_qmean.py b/docker/run_qmean.py
index 15e21a2..b3984eb 100755
--- a/docker/run_qmean.py
+++ b/docker/run_qmean.py
@@ -140,19 +140,19 @@ def _run_accpro(fasta_file, msa, workdir, seqlen):
if "Segmentation fault" in sout:
LogError(
'Running ACCPro failed for command "%s" with a segmentation fault'
- % command
+ % " ".join(cmd)
)
return None
if "Segmentation fault" in serr:
LogError(
'Running ACCPro failed for command "%s" with a segmentation fault'
- % command
+ % " ".join(cmd)
)
return None
if job.returncode != 0:
LogError(
'Running ACCPro failed for command "%s":\n%s\n%s'
- % (" ".join(command), sout, serr)
+ % (" ".join(cmd), sout, serr)
)
return None
--
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