From 8c0f4f42538b8c4d73b7d1647fc66a2fc963bea0 Mon Sep 17 00:00:00 2001 From: andrewjpage Date: Mon, 1 Jul 2013 13:42:28 +0100 Subject: [PATCH] delete intermediate raxml files if they already exist --- run_gubbins.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/run_gubbins.py b/run_gubbins.py index 7676db2d..a12777dd 100755 --- a/run_gubbins.py +++ b/run_gubbins.py @@ -552,6 +552,12 @@ def use_bundled_exec(input_executable, bundled_executable): current_tree_name = "" max_iteration = 1 + +# cleanup RAxML intermediate files +if args.no_cleanup == 0 or args.no_cleanup is None: + raxml_regex_for_file_deletions = raxml_regex_for_file_deletions(base_filename_without_ext,current_time,starting_base_filename, args.iterations) + delete_files_based_on_list_of_regexes('.', raxml_regex_for_file_deletions, args.verbose) + for i in range(1, args.iterations+1): max_iteration += 1