Improve logging error subprocess handling

ppanggolin/cluster/cluster.py

@@ -135,8 +135,7 @@ def align_rep(faa_file: Path, tmpdir: Path, cpu: int = 1, coverage: float = 0.8,
 
     :return: Result of alignment
     """
-    seqdb = create_mmseqs_db(faa_file, 'rep_sequence_db', tmpdir, db_mode=1, db_type=1)
-    cmd = list(map(str, ["mmseqs", "createdb", "--createdb-mode", 1, faa_file, seqdb]))
+    seqdb = create_mmseqs_db([faa_file], 'rep_sequence_db', tmpdir, db_mode=1, db_type=1)
     logging.getLogger("PPanGGOLiN").info("Aligning cluster representatives...")
     alndb = tmpdir / 'rep_alignment_db'
     cmd = list(map(str, ["mmseqs", "search", seqdb, seqdb, alndb, tmpdir, "-a", "--min-seq-id", identity,

ppanggolin/utils.py

@@ -1187,13 +1187,13 @@ def get_consecutive_region_positions(region_positions: List[int], contig_gene_co
 
 def run_subprocess(cmd: List[str], output: Path = None, msg: str = "Subprocess failed with the following error:\n"):
     logging.getLogger("PPanGGOLiN").debug(" ".join(cmd))
-    if output is None:
-        result = subprocess.run(cmd, stdout=subprocess.DEVNULL, check=True)
+    try:
+        result = subprocess.run(cmd, check=True, capture_output=True, text=True)
+    except subprocess.CalledProcessError as subprocess_err:
+        for line in subprocess_err.stdout.split("\n"):
+            logging.getLogger("PPanGGOLiN").error(line)
+        raise Exception(msg + subprocess_err.stderr)
     else:
-        result = subprocess.run(cmd, capture_output=True, check=True)
-
-    with open(output, "w") as fout:
-        fout.write(result.stdout.decode('utf-8'))
-
-    if result.stderr and result.returncode != 0:
-        raise Exception(msg + f"{result.stderr.decode('utf-8')}")
+        if output is not None:
+            with open(output, 'w') as fout:
+                fout.write(result.stdout)