inprogress

[jalview.git] / forester / ruby / evoruby / exe / run_phylo_pipeline_x.rb

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 (file)
--- 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