diff --git a/src/reference.snake b/src/reference.snake
index a2e826a..f88a161 100644
--- a/src/reference.snake
+++ b/src/reference.snake
@@ -20,7 +20,7 @@ rule reference_download:
     'Downloading gencode transcriptome reference.'
   shell:
     """
-    zcat {input} > {output}
+    zcat -f {input} > {output}
     """
 
 if 'spikeIns' in config.get('reference', {}):
@@ -35,7 +35,7 @@ if 'spikeIns' in config.get('reference', {}):
       'Adding spike-in sequences to gencode transcriptome reference'
     shell:
       """
-      cat {input.ref} {input.spike} > {output}
+      zcat -f {input.ref} {input.spike} > {output}
       """
 
 rule tx2gene_from_fasta: