diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py index 1931a79219451ee58a21cb48a4fc4f0832455a34..d40eb9c7bbf043665fcf898f42b7d0443d0a1cb5 100755 --- a/PanACoTA/utils.py +++ b/PanACoTA/utils.py @@ -309,7 +309,7 @@ def run_cmd(cmd, error, eof=False, **kwargs): call.wait() retcode = call.returncode except OSError: - logger.error(error + ": " + "{} does not exist".format(cmd)) + logger.error("error : {cmd} does not exist") if eof: sys.exit(1) else: @@ -392,14 +392,14 @@ def write_warning_skipped(skipped, do_format=False, prodigal_only=False, logfile logger = logging.getLogger("utils") list_to_write = "\n".join(["\t- " + genome for genome in skipped]) if not do_format: - logger.info("WARNING: Some genomes could not be annotated. See {0}".format(logfile)) - logger.warning("{0} had problems while annotating some genomes, or " + logger.info(f"WARNING: Some genomes could not be annotated. See {soft}") + logger.warning(f"{soft} had problems while annotating some genomes, or " "did not find any gene. Hence, they are not formatted, and absent " "from your output database. Please look at the " "current error log " "(<output_directory>/PanACoTA-annotate_list_genomes[-date].log.err) to get more " "information on the problems. Here are those " - "genomes:\n {1}".format(soft, list_to_write)) + "genomes:\n{list_to_write}") else: logger.info(f"WARNING: Some genomes could not be formatted. See {logfile}") logger.warning(("Some genomes were annotated by {0}, but could not be formatted, " @@ -447,7 +447,6 @@ def write_genomes_info(genomes, kept_genomes, list_file, res_path, qc=False): logger.info("{} genomes were discarded.".format(nb_disc)) # Get input list file name (without path) _, name_lst = os.path.split(list_file) - # if not QC, write discarded genomes to a file "discarded-[list_file].lst" if not qc: outdisc = os.path.join(res_path,