diff --git a/tools/strainphlan/sample2markers/Snakefile b/tools/strainphlan/sample2markers/Snakefile
index c9ee84c85b4717ae1fb08db8eba516f216e1abfb..a577299e5c97449bcb683cac9ccd4a8f31f8fc31 100644
--- a/tools/strainphlan/sample2markers/Snakefile
+++ b/tools/strainphlan/sample2markers/Snakefile
@@ -8,11 +8,11 @@ rule sample2markers:
     input:
         __sample2markers_input
     output:
-        dir = __sample2markers_output_dir,
-        file = __sample2markers_output
+        __sample2markers_output
     params:
         exec_command = __sample2markers_exec_command,
         modules = __sample2markers_modules,
+        output_dir = __sample2markers_output_dir,
         options = __sample2markers_options
     threads:
         __sample2markers_threads
@@ -20,5 +20,5 @@ rule sample2markers:
         command = []
         if params.modules:
             command.append("module load {params.modules}")
-        command.append("{params.exec_command} -n {threads} {params.options} -i {input} -o {output.dir}")
+        command.append("{params.exec_command} -n {threads} {params.options} -i {input} -o {params.output_dir}")
         shell(" && ".join(command))