X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Fexe%2Frun_phylo_pipeline_x.rb;h=b13581ac5154ca5ccd9d35ff80c6a893184140c5;hb=9ad4eb52d172607313ea119d7a33992258632b95;hp=8d0a27d6490f5c850a23acb8811fcf5ea72dfdb1;hpb=81aff14b756ba3fd6341875c4e4af92f0415450a;p=jalview.git

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
index 8d0a27d..b13581a 100644
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
@@ -131,10 +131,10 @@ module Evoruby
           if LAUNCH_ANALYSIS
             puts "f. analysis:"
             Dir.chdir "#{hmm_name}/msa/"
-            run_command "#{PF} -s"
+            run_command "#{PF} -b=1 -s"
             Dir.chdir "../.."
             Dir.chdir "#{hmm_name}/msa100/"
-            run_command "#{PF} -s"
+            run_command "#{PF} -b=100 -s"
             Dir.chdir "../.."
             puts
           end