From c9b9337aa8d53de828c5e707165431a8592f87b3 Mon Sep 17 00:00:00 2001 From: Amandine PERRIN <amandine.perrin@pasteur.fr> Date: Fri, 29 Jan 2021 09:36:50 +0100 Subject: [PATCH] modify error message when cmd fails --- PanACoTA/pangenome_module/mmseqs_functions.py | 4 ++-- PanACoTA/utils.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/PanACoTA/pangenome_module/mmseqs_functions.py b/PanACoTA/pangenome_module/mmseqs_functions.py index af42e1aa..ac93d92e 100755 --- a/PanACoTA/pangenome_module/mmseqs_functions.py +++ b/PanACoTA/pangenome_module/mmseqs_functions.py @@ -417,8 +417,8 @@ def create_mmseqs_db(mmseqdb, prt_path, logmmseq): return 0 if len(files_existing) != len(outext): logger.info("Creating database") - logger.details("Existing files: {}".format(len(files_existing))) - logger.details("Expected extensions: {}".format(len(outext))) + logger.debug("Existing files: {}".format(len(files_existing))) + logger.debug("Expected extensions: {}".format(len(outext))) cmd = f"mmseqs createdb {prt_path} {mmseqdb}" msg = (f"Problem while trying to convert database {prt_path} to mmseqs " "database format.") diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py index 11a099d2..4d9f3a09 100755 --- a/PanACoTA/utils.py +++ b/PanACoTA/utils.py @@ -341,7 +341,7 @@ def run_cmd(cmd, error, eof=False, **kwargs): call.wait() retcode = call.returncode except OSError: - logger.error(f"error: {cmd} does not exist") + logger.error(f"error: command {cmd} is not possible.") if eof: sys.exit(1) else: -- GitLab