diff --git a/sentieon_cli/dnascope.py b/sentieon_cli/dnascope.py
index 264709c..57ae007 100644
--- a/sentieon_cli/dnascope.py
+++ b/sentieon_cli/dnascope.py
@@ -34,15 +34,18 @@
     SVSolver,
     WgsMetricsAlgo,
 )
+from .logging import get_logger
 from .util import (
     __version__,
     check_version,
     library_preloaded,
-    logger,
     path_arg,
     tmp,
 )
 
+logger = get_logger(__name__)
+
+
 ALN_MIN_VERSIONS = {
     "sentieon driver": packaging.version.Version("202308"),
     "samtools": packaging.version.Version("1.16"),
@@ -651,7 +654,7 @@ def dnascope(
     assert model_bundle
     assert str(output_vcf).endswith(".vcf.gz")
 
-    logger.setLevel(kwargs["loglevel"])
+    logger.parent.setLevel(kwargs["loglevel"])
     logger.info("Starting sentieon-cli version: %s", __version__)
 
     if not library_preloaded("libjemalloc.so"):
diff --git a/sentieon_cli/dnascope_longread.py b/sentieon_cli/dnascope_longread.py
index 2474364..fea6fd2 100644
--- a/sentieon_cli/dnascope_longread.py
+++ b/sentieon_cli/dnascope_longread.py
@@ -25,15 +25,18 @@
     RepeatModel,
     VariantPhaser,
 )
+from .logging import get_logger
 from .util import (
     __version__,
     check_version,
-    logger,
     path_arg,
     tmp,
     library_preloaded,
 )
 
+logger = get_logger(__name__)
+
+
 TOOL_MIN_VERSIONS = {
     "sentieon driver": packaging.version.Version("202308.01"),
     "bcftools": packaging.version.Version("1.10"),
@@ -549,10 +552,10 @@ def mosdepth(
             )
             return 1
 
-    mosdepth_dir = pathlib.Path(
-        str(output_vcf).replace(".vcf.gz", "_mosdepth")
-    )
-    for input_file in sample_input:
+    for i, input_file in enumerate(sample_input):
+        mosdepth_dir = pathlib.Path(
+            str(output_vcf).replace(".vcf.gz", f"_mosdepth_{i}")
+        )
         run(
             cmds.cmd_mosdepth(
                 input_file,
@@ -734,7 +737,7 @@ def dnascope_longread(
     assert model_bundle
     assert str(output_vcf).endswith(".vcf.gz")
 
-    logger.setLevel(kwargs["loglevel"])
+    logger.parent.setLevel(kwargs["loglevel"])
     logger.info("Starting sentieon-cli version: %s", __version__)
 
     if not library_preloaded("libjemalloc.so"):
diff --git a/sentieon_cli/runner.py b/sentieon_cli/runner.py
index 2596664..bba8dfb 100644
--- a/sentieon_cli/runner.py
+++ b/sentieon_cli/runner.py
@@ -9,7 +9,7 @@
 
 def run(cmd: str):
     """Run a command."""
-    logger.info("running: %s", cmd)
+    logger.info("running command: %s", cmd)
     t0 = time.time()
     sp.run(
         cmd,