diff --git a/modules/local/counts/calculate_tpm/templates/calculate_tpm.py b/modules/local/counts/calculate_tpm/templates/calculate_tpm.py
index 8dad632..730d0ba 100755
--- a/modules/local/counts/calculate_tpm/templates/calculate_tpm.py
+++ b/modules/local/counts/calculate_tpm/templates/calculate_tpm.py
@@ -34,7 +34,10 @@ def format_yaml_like(data: dict, indent: int = 0) -> str:
 df_lengths = df_lengths / 1e3
 df_lengths = df_lengths.groupby(df_lengths.index).mean()
 
-df_lengths = df_lengths.loc[df_lengths.index.isin(df_counts.index)]
+# Subset gene lengths and counts to common index
+shared_index = df_lengths.index.intersection(df_counts.index)
+df_lengths = df_lengths.loc[shared_index]
+df_counts = df_counts.loc[shared_index]
 
 # Calculate TPM
 df_rpk = df_counts.div(df_lengths["length"], axis=0)