diff --git a/phylogenetic/defaults/hmpxv1/config.yaml b/phylogenetic/defaults/hmpxv1/config.yaml index 40ce633..39b29c0 100644 --- a/phylogenetic/defaults/hmpxv1/config.yaml +++ b/phylogenetic/defaults/hmpxv1/config.yaml @@ -67,7 +67,7 @@ subsample: - B.1.23 b1: group_by: "--group-by country year" - sequences_per_group: "--subsample-max-sequences 100" + sequences_per_group: "--subsample-max-sequences 300" other_filters: "--exclude-where outbreak!=hMPXV-1 clade!=IIb" ## align diff --git a/phylogenetic/rules/construct_phylogeny.smk b/phylogenetic/rules/construct_phylogeny.smk index 4ce598f..c33ddeb 100644 --- a/phylogenetic/rules/construct_phylogeny.smk +++ b/phylogenetic/rules/construct_phylogeny.smk @@ -30,7 +30,6 @@ rule tree: augur tree \ --alignment {input.alignment} \ --exclude-sites {input.tree_mask} \ - --tree-builder-args="-redo" \ --output {output.tree} \ --nthreads {threads} """