X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fphylogenies_decorator.rb;h=1eea808704e646c8b56b43306940e43f07f4ff79;hb=2d569f0ff0e0c8fa5d21ca6b3446a152132ff1de;hp=6d501746e6b8d4fe90822018e020843d6b2fc0e9;hpb=7a7e1f4dfe7394192db4e1239327a0a8af410997;p=jalview.git

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index 6d50174..1eea808 100644
--- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@ -200,22 +200,34 @@ module Evoruby
           end
 
           cmd = decorator +
-           ' -p -f=m ' + phylogeny_file + ' ' +
+           ' -t -p -f=m ' + phylogeny_file + ' ' +
            seqs_file_name  + ' ' + TMP_FILE_1
           puts cmd
-          execute_cmd( cmd, log )
+          begin
+            execute_cmd( cmd, log )
+          rescue Error
+            Util.fatal_error( PRG_NAME, 'error: ' + $! )
+          end
 
           cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
            '-f=d ' + TMP_FILE_1 + ' ' +
            domains_mapfile_name + ' ' +TMP_FILE_2
           puts cmd
-          execute_cmd( cmd, log )
+          begin
+            execute_cmd( cmd, log )
+          rescue Error
+            Util.fatal_error( PRG_NAME, 'error: ' + $! )
+          end
 
           cmd = decorator + ' ' +  DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
            '-f=n ' + TMP_FILE_2 + ' ' +
            ids_mapfile_name + ' ' + outfile
           puts cmd
-          execute_cmd( cmd, log )
+          begin
+            execute_cmd( cmd, log )
+          rescue Error
+            Util.fatal_error( PRG_NAME, 'error: ' + $! )
+          end
 
           File.delete( TMP_FILE_1 )
           File.delete( TMP_FILE_2 )