diff --git a/ppanggolin/cluster/cluster.py b/ppanggolin/cluster/cluster.py index c30cac84..ab1046b9 100644 --- a/ppanggolin/cluster/cluster.py +++ b/ppanggolin/cluster/cluster.py @@ -398,7 +398,7 @@ def read_clustering(pangenome: Pangenome, families_tsv_file: Path, infer_singlet :param disable_bar: Allow to disable progress bar """ check_pangenome_former_clustering(pangenome, force) - check_pangenome_info(pangenome, need_annotations=True, need_gene_sequences=write_sequences, disable_bar=disable_bar) + check_pangenome_info(pangenome, need_annotations=True, need_gene_sequences=True, disable_bar=disable_bar) logging.getLogger("PPanGGOLiN").info(f"Reading {families_tsv_file.name} the gene families file ...") filesize = os.stat(families_tsv_file).st_size @@ -455,8 +455,7 @@ def read_clustering(pangenome: Pangenome, families_tsv_file: Path, infer_singlet pangenome.status["genesClustered"] = "Computed" if frag: # if there was fragment information in the file. pangenome.status["defragmented"] = "Computed" - if write_sequences: - pangenome.status["geneFamilySequences"] = "Computed" + pangenome.status["geneFamilySequences"] = "Computed" pangenome.parameters["cluster"] = {} pangenome.parameters["cluster"]["# read_clustering_from_file"] = True pangenome.parameters["cluster"]["infer_singletons"] = infer_singleton