diff --git a/snakePipes/shared/rules/createIndices.snakefile b/snakePipes/shared/rules/createIndices.snakefile
index 45035c2ee..f383fe5c8 100755
--- a/snakePipes/shared/rules/createIndices.snakefile
+++ b/snakePipes/shared/rules/createIndices.snakefile
@@ -54,7 +54,7 @@ else:
         params:
             spikeinExt = spikeinExt
         shell: """
-            sed '/\s+/$/{spikeinExt} /' {input} > {output}
+            sed 's/\s\+/{params.spikeinExt} /' {input} > {output}
         """
 
     rule createGenomeFasta: