Better logging of FastTree

metagenopolis · Mar 28, 2024 · 426a53c · 426a53c
1 parent 74ed5a1
commit 426a53c
Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/meteor/phylogeny.py b/meteor/phylogeny.py
@@ -105,7 +105,8 @@ def execute(self) -> None:
         # Start phylogenies
         start = perf_counter()
         tree_files: list[Path] = []
-        for msp_file in self.msp_file_list:
+        msp_count = len(self.msp_file_list)
+        for idx, msp_file in enumerate(self.msp_file_list, start=1):
             with NamedTemporaryFile(
                 mode="wt", dir=self.meteor.tmp_dir, suffix=".fasta", delete=False
             ) as temp_clean:
@@ -115,7 +116,7 @@ def execute(self) -> None:
                 with tree_file.open("wt", encoding="UTF-8") as tree:
                     os.environ["OMP_NUM_THREADS"] = str(self.meteor.threads)
                     # Compute trees
-                    call(
+                    result = call(
                         [
                             "FastTree",
                             "-nt",
@@ -124,7 +125,10 @@ def execute(self) -> None:
                         ],
                         stdout=tree,
                     )
+                    if result != 0:
+                        logging.error("FastTree failed with return code %d", result)
                     tree_files.append(tree_file)
+            logging.info("Completed MSP tree %d/%d", idx, msp_count)
         logging.info("Completed phylogeny in %f seconds", perf_counter() - start)
         config = self.set_tree_config(fasttree_version, tree_files)
         self.save_config(config, self.meteor.tree_dir / "census_stage_4.json")