diff --git a/lib/Interface/scripts/processSubmit.pl b/lib/Interface/scripts/processSubmit.pl
index 3cfec24..499ca50 100755
--- a/lib/Interface/scripts/processSubmit.pl
+++ b/lib/Interface/scripts/processSubmit.pl
@@ -131,11 +131,11 @@ sub _launchPanseq{
             blastDirectory     => $serverSettings->{'blastDirectory'},
             numberOfCores      => $serverSettings->{'numberOfCores'},
             baseDirectory      => $resultsDir,
-            minimumNovelRegionSize => $serverSettings->{'minimumNovelRegionSize'},
+            minimumNovelRegionSize => $cgi->param('minimumNovelRegionSize'),
             numberOfCores      => $serverSettings->{'numberOfCores'},
             muscleExecutable   => $serverSettings->{'muscleExecutable'},
             outputDirectory    => $newDir,
-            percentIdentityCutoff => $serverSettings->{'percentIdentityCutoff'},
+            percentIdentityCutoff => $cgi->param('percentIdentityCutoff'),
             nucB               => $cgi->param( 'nucB' ),
             nucC               => $cgi->param( 'nucC' ),
             nucD               => $cgi->param( 'nucD' ),