diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py index ddc057da5dbf7218826cc5e98c7f69ca8f3eb40c..5aebd0fe98bf74643a9e02a0429ad5f095c8260a 100644 --- a/PanACoTA/subcommands/prepare.py +++ b/PanACoTA/subcommands/prepare.py @@ -395,10 +395,13 @@ def check_args(parser, args): if args.no_refseq and not args.outdir: parser.error("You must provide an output directory, where your results will be saved.") - # If user wants only mash steps, check that he gave info file + # If user wants only mash steps, check that he gave info file, and outdir if args.only_mash and not args.from_info: parser.error("If you want to run only Mash filtering steps, please give the " "info file with the required information (see '--info' option)") + if args.only_mash and not args.outdir: + parser.error("If you want to run only Mash filtering steps, please give the " + "output directory where you want to save your results (see '-o' option)") # Cannot be verbose and quiet at the same time if args.verbose > 0 and args.quiet: