From 7bbdc87ed56bf1fa464964bc0ec2d28ca9f2e03a Mon Sep 17 00:00:00 2001 From: Amine GHOZLANE Date: Mon, 24 Jun 2024 11:34:49 +0200 Subject: [PATCH] Clarify execution message --- meteor/phylogeny.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/meteor/phylogeny.py b/meteor/phylogeny.py index 85c35e9..9ae2f07 100644 --- a/meteor/phylogeny.py +++ b/meteor/phylogeny.py @@ -223,8 +223,13 @@ def execute(self) -> None: # mycluster.write( # tree_file.with_suffix(".tree"), # ) - tree_files.append(tree_file) - logging.info("Completed MSP tree %d/%d", idx, msp_count) + if tree_file.exists(): + tree_files.append(tree_file) + logging.info("Completed MSP tree %d/%d", idx, msp_count) + else: + logging.info( + "No tree file generated for MSP %s, skipping", msp_file.name + ) logging.info("Completed phylogeny in %f seconds", perf_counter() - start) config = self.set_tree_config(raxml_ng_version, tree_files) self.save_config(config, self.meteor.tree_dir / "census_stage_4.json")