udpate

Author: LifeWorks

Makefile

@@ -106,13 +106,13 @@ evolve : FORCE
 	@echo "ANC_HOME =" $(ANC_HOME)
 	@echo "FACILE_HOME =" $(FACILE_HOME)
 	mkdir -p $(basename $(config))
-	$(BIOJAZZ_HOME)/biojazz.pl --config=config/$(config) --tag=$(tag) --cluster_type=$(cluster_type) --cluster_size=$(cluster_size) --seed=$(seed) 2>&1 | tee -a -i $(basename $(config))/$(basename $(config)).$(tag).log
+	$(BIOJAZZ_HOME)/biojazz.pl --verbosity=0 --config=config/$(config) --tag=$(tag) --cluster_type=$(cluster_type) --cluster_size=$(cluster_size) --seed=$(seed) 2>&1 | tee -a -i $(basename $(config))/$(basename $(config)).$(tag).log
 
 evolve_rescore : FORCE
 	@echo "ANC_HOME =" $(ANC_HOME)
 	@echo "FACILE_HOME =" $(FACILE_HOME)
 	mkdir -p $(basename $(config))
-	$(BIOJAZZ_HOME)/biojazz.pl --config=config/$(config) --tag=$(tag) --cluster_type=$(cluster_type) --cluster_size=$(cluster_size) --rescore --seed=$(seed) 2>&1 | tee -a -i $(basename $(config))/$(basename $(config)).$(tag).log
+	$(BIOJAZZ_HOME)/biojazz.pl --verbosity=0 --config=config/$(config) --tag=$(tag) --cluster_type=$(cluster_type) --cluster_size=$(cluster_size) --rescore --seed=$(seed) 2>&1 | tee -a -i $(basename $(config))/$(basename $(config)).$(tag).log
 
 
 score : FORCE

custom/Adaptive.pm

@@ -357,7 +357,7 @@ use base qw(Scoring);
                     SS_timescale => $config_ref->{SS_timescale},
                 );
                 burp_file("$matlab_work/$genome_name.mod", $anc_model);
-                system("$ENV{ANC_HOME}/anc.pl --report=species $matlab_work/$genome_name.mod");
+                system("$ENV{ANC_HOME}/anc.pl --verbosity=0 --report=species $matlab_work/$genome_name.mod");
                 my @facile_model = slurp_file("$matlab_work/$genome_name.eqn");
 
                 $stats_ref->{species_report_flag} = $self->anc_process_species_report("$matlab_work/$genome_name.species.rpt");