diff --git a/Snakefile b/Snakefile
index 4b8811b50c9331db5ea7d165b6b71af6f706b14a..5333337e270e16943bfdc1524bae1086816eb911 100644
--- a/Snakefile
+++ b/Snakefile
@@ -324,8 +324,9 @@ rule combine_strandphaser_output:
         "strand_states/" + config["sample"] + ".strandphaser_output.txt"
     shell:
         """
-        cat {input} | head -n1 > {output}
-        for x in {input}; do tail -n+2 $x >> {output}; done
+        set +o pipefail
+        cat {input} | head -n1 > {output};
+        for x in {input}; do tail -n+2 $x >> {output}; done;
         """