Include in try-catch blocks with error message

src/chanjo2/meta/handle_completeness_stats.py

@@ -1,39 +1,45 @@
+import logging
 import subprocess
 import tempfile
 from typing import Dict, List, Tuple
 
 CHROM_INDEX = 0
 START_INDEX = 1
 STOP_INDEX = 2
+LOG = logging.getLogger(__name__)
 
 
 def get_d4tools_intervals_completeness(
     d4_file_path: str, bed_file_path: str, completeness_thresholds: List[int]
 ) -> List[Dict]:
     """Return coverage completeness over all intervals of a bed file using the perc_cov d4tools command."""
     threshold_stats = []
-    d4tools_stats_perc_cov: str = subprocess.check_output(
-        [
-            "d4tools",
-            "stat",
-            "-s",
-            f"perc_cov={','.join(str(threshold) for threshold in completeness_thresholds)}",
-            "--region",
-            bed_file_path,
-            d4_file_path,
-        ],
-        text=True,
-    )
-    for line in d4tools_stats_perc_cov.splitlines():
-        stats_dict: Dict = dict(
-            (
-                zip(
-                    completeness_thresholds,
-                    [float(stat) for stat in line.rstrip().split("\t")[3:]],
+    try:
+        d4tools_stats_perc_cov: str = subprocess.check_output(
+            [
+                "d4tools",
+                "stat",
+                "-s",
+                f"perc_cov={','.join(str(threshold) for threshold in completeness_thresholds)}",
+                "--region",
+                bed_file_path,
+                d4_file_path,
+            ],
+            text=True,
+        )
+
+        for line in d4tools_stats_perc_cov.splitlines():
+            stats_dict: Dict = dict(
+                (
+                    zip(
+                        completeness_thresholds,
+                        [float(stat) for stat in line.rstrip().split("\t")[3:]],
+                    )
                 )
             )
-        )
-        threshold_stats.append(stats_dict)
+            threshold_stats.append(stats_dict)
+    except subprocess.CalledProcessError, e:
+        LOG.error(f"d4tools stat -s perc_cov failed with the following error:{e}")
 
     return threshold_stats