diff --git a/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java b/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java index 14f58925db2f77fb45faa1ea979e6ef4f0b03448..19cb69582b3c270bb6529aa7686c5f34473b6466 100644 --- a/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java +++ b/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java @@ -2091,10 +2091,6 @@ public class Phylogeny { check_if_single_copy_groups = true; } single_copy_input_file = SELECTED_HMGROUPS; - report_number_of_threads(true, true); // prints how many threads were selected by user - if (PHENOTYPE == null) { - System.out.println("No --phenotype was provided, tree will only contain genome numbers"); - } try (Transaction tx = graphDb.beginTx()) { // start database transaction Node pangenome_node = graphDb.findNodes(pangenome_label).next(); @@ -2116,7 +2112,7 @@ public class Phylogeny { MultipleSequenceAlignment msa = new MultipleSequenceAlignment( msaMethod, false, - false, + true, true ); System.out.println(); @@ -2461,7 +2457,7 @@ public class Phylogeny { MultipleSequenceAlignment msa = new MultipleSequenceAlignment( "per_group", false, - false, + true, false ); msa.alignSequences(true, false); @@ -2808,12 +2804,12 @@ public class Phylogeny { */ public String check_mode_for_snp_tree() { String alignment_phylogeny_mode = ""; - if (Mode.equals("0")) { // no --mode was provided + if (Mode.equals("0")) { // no --clustering-method was provided if (PROTEOME) { - System.out.println("\rNo --mode selected. Preparing Maximum Likelihood phylogeny for protein sequences"); + System.out.println("\rNo --clustering-method selected. Preparing Maximum Likelihood phylogeny for protein sequences"); alignment_phylogeny_mode = "ML,protein"; } else { // pangenome - System.out.println("\rNo --mode selected. Preparing Maximum Likelihood phylogeny for nucleotide sequences"); + System.out.println("\rNo --clustering-method selected. Preparing Maximum Likelihood phylogeny for nucleotide sequences"); alignment_phylogeny_mode = "ML,nucleotide"; } } else if (CLUSTERING_METHOD.equals("NJ")) { @@ -2833,7 +2829,7 @@ public class Phylogeny { alignment_phylogeny_mode = "ML,nucleotide"; } } else { - System.out.println("\rThe provided --mode argument is not recognized"); + System.out.println("\rThe provided --clustering-method argument is not recognized"); System.exit(1); }