diff --git a/workflow/tests/test_annotate_peaks.py b/workflow/tests/test_annotate_peaks.py
index e69813332281cc5a72983e35cbdc565cc2ded5d3..fa5c2411fccd7784d780c5699b2b9de541e84064 100644
--- a/workflow/tests/test_annotate_peaks.py
+++ b/workflow/tests/test_annotate_peaks.py
@@ -25,4 +25,4 @@ def test_annotate_peaks_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_upsetplot.pdf'))
     annotation_file = test_output_path + 'ENCSR729LGA.chipseeker_annotation.csv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 25614
+    assert utils.count_lines(annotation_file) == 25391
diff --git a/workflow/tests/test_overlap_peaks.py b/workflow/tests/test_overlap_peaks.py
index 36ed3da17e7eb61aa4440ae18527453d19a32df9..99d43b87939617c801bad0389f14e2683cde0f82 100644
--- a/workflow/tests/test_overlap_peaks.py
+++ b/workflow/tests/test_overlap_peaks.py
@@ -44,4 +44,4 @@ def test_overlap_peaks_singleend():
 def test_overlap_peaks_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.rejected.narrowPeak'))
     peak_file = test_output_path + 'ENCSR729LGA.replicated.narrowPeak'
-    assert utils.count_lines(peak_file) == 25878
+    assert utils.count_lines(peak_file) == 25655