diff --git a/aviary/modules/binning/scripts/finalise_stats.py b/aviary/modules/binning/scripts/finalise_stats.py
index b16e3038..0b519cf7 100644
--- a/aviary/modules/binning/scripts/finalise_stats.py
+++ b/aviary/modules/binning/scripts/finalise_stats.py
@@ -85,8 +85,8 @@ def get_taxonomy(rename_columns="Bin Id"):
 
     taxa = get_taxonomy(checkm_output.columns[0])
 
-    merged_out = pd.merge(checkm_output, coverage_file, on=[checkm_output.columns[0]])
-    merged_out = pd.merge(merged_out, taxa, on=[checkm_output.columns[0]])
+    merged_out = pd.merge(checkm_output, coverage_file, on=[checkm_output.columns[0]], how="left")
+    merged_out = pd.merge(merged_out, taxa, on=[merged_out.columns[0]], how="left")
     merged_out.to_csv(snakemake.output.bin_stats, sep='\t', index=False)
 
     checkm_minimal = checkm_output[["Bin Id",  "Marker lineage",  "# genomes", "# markers", "# marker sets",
diff --git a/test/test_integration.py b/test/test_integration.py
index e0e4e0a2..1623e7fa 100755
--- a/test/test_integration.py
+++ b/test/test_integration.py
@@ -77,7 +77,12 @@ def test_short_read_recovery(self):
             )
             subprocess.run(cmd, shell=True, check=True)
 
-            self.assertTrue(os.path.isfile(f"{tmpdir}/aviary_out/bins/bin_info.tsv"))
+            bin_info_path = f"{tmpdir}/aviary_out/bins/bin_info.tsv"
+            self.assertTrue(os.path.isfile(bin_info_path))
+            with open(bin_info_path) as f:
+                num_lines = sum(1 for _ in f)
+            self.assertTrue(num_lines > 1)
+
             self.assertTrue(os.path.isfile(f"{tmpdir}/aviary_out/data/final_contigs.fasta"))
             self.assertTrue(os.path.islink(f"{tmpdir}/aviary_out/assembly/final_contigs.fasta"))
 
@@ -97,7 +102,11 @@ def test_short_read_recovery_skip_binners(self):
             )
             subprocess.run(cmd, shell=True, check=True)
 
-            self.assertTrue(os.path.isfile(f"{tmpdir}/aviary_out/bins/bin_info.tsv"))
+            bin_info_path = f"{tmpdir}/aviary_out/bins/bin_info.tsv"
+            self.assertTrue(os.path.isfile(bin_info_path))
+            with open(bin_info_path) as f:
+                num_lines = sum(1 for _ in f)
+            self.assertTrue(num_lines > 1)
             self.assertFalse(os.path.isfile(f"{tmpdir}/aviary_out/data/final_contigs.fasta"))
 
 
@@ -117,7 +126,12 @@ def test_short_read_recovery_skip_abundances(self):
             )
             subprocess.run(cmd, shell=True, check=True)
 
-            self.assertTrue(os.path.isfile(f"{tmpdir}/aviary_out/bins/bin_info.tsv"))
+            bin_info_path = f"{tmpdir}/aviary_out/bins/bin_info.tsv"
+            self.assertTrue(os.path.isfile(bin_info_path))
+            with open(bin_info_path) as f:
+                num_lines = sum(1 for _ in f)
+            self.assertEqual(num_lines, 3)
+
             self.assertFalse(os.path.isfile(f"{tmpdir}/aviary_out/data/final_contigs.fasta"))