+ cmd = decorator +
+ ' -p -f=m ' + phylogeny_file + ' ' +
+ seqs_file_name + ' ' + TMP_FILE_1
+ puts cmd
+ execute_cmd( cmd, log )
+
+ cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
+ '-f=d ' + TMP_FILE_1 + ' ' +
+ domains_mapfile_name + ' ' +TMP_FILE_2
+ puts cmd
+ execute_cmd( cmd, log )
+
+ cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
+ '-f=n ' + TMP_FILE_2 + ' ' +
+ ids_mapfile_name + ' ' + outfile
+ puts cmd
+ execute_cmd( cmd, log )
+
+ File.delete( TMP_FILE_1 )
+ File.delete( TMP_FILE_2 )
+