From 5ae7e578d034ebcca9a2729220bef98b9f6027b7 Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Sat, 20 Jan 2024 20:16:56 +0100
Subject: [PATCH 1/2] Use mutations rather than mutations-per-site for clade
 IIb/B.1 builds

For clade IIb/B.1. divergence is on the order of 1/10000 per site or less 10-100 mutations
---
 phylogenetic/config/hmpxv1/config.yaml         | 1 +
 phylogenetic/config/hmpxv1_big/config.yaml     | 1 +
 phylogenetic/config/mpxv/config.yaml           | 1 +
 phylogenetic/workflow/snakemake_rules/core.smk | 3 ++-
 4 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/phylogenetic/config/hmpxv1/config.yaml b/phylogenetic/config/hmpxv1/config.yaml
index 078d9309..a9b6739a 100644
--- a/phylogenetic/config/hmpxv1/config.yaml
+++ b/phylogenetic/config/hmpxv1/config.yaml
@@ -70,6 +70,7 @@ timetree: true
 root: "MK783032 MK783030"
 clock_rate: 5.7e-5
 clock_std_dev: 2e-5
+divergence_units: "mutations"
 
 ## recency
 recency: true
diff --git a/phylogenetic/config/hmpxv1_big/config.yaml b/phylogenetic/config/hmpxv1_big/config.yaml
index d92c7385..513e530f 100644
--- a/phylogenetic/config/hmpxv1_big/config.yaml
+++ b/phylogenetic/config/hmpxv1_big/config.yaml
@@ -49,6 +49,7 @@ timetree: true
 root: "OP890401"
 clock_rate: 5.7e-5
 clock_std_dev: 2e-5
+divergence_units: "mutations"
 
 ## recency
 recency: true
diff --git a/phylogenetic/config/mpxv/config.yaml b/phylogenetic/config/mpxv/config.yaml
index 40b950f3..d569445a 100644
--- a/phylogenetic/config/mpxv/config.yaml
+++ b/phylogenetic/config/mpxv/config.yaml
@@ -66,6 +66,7 @@ timetree: false
 root: "min_dev"
 clock_rate: 3e-6
 clock_std_dev: 6e-6
+divergence_units: "mutations-per-site"
 
 ## recency
 recency: true
diff --git a/phylogenetic/workflow/snakemake_rules/core.smk b/phylogenetic/workflow/snakemake_rules/core.smk
index 598a3bba..474f3a7b 100644
--- a/phylogenetic/workflow/snakemake_rules/core.smk
+++ b/phylogenetic/workflow/snakemake_rules/core.smk
@@ -221,7 +221,6 @@ rule refine:
         - use {params.coalescent} coalescent timescale
         - estimate {params.date_inference} node dates
         - filter tips more than {params.clock_filter_iqd} IQDs from clock expectation
-    Note: --use-fft was removed (temporarily) due to https://github.com/neherlab/treetime/issues/242
     """
     input:
         tree=rules.fix_tree.output.tree
@@ -244,6 +243,7 @@ rule refine:
         if "clock_std_dev" in config
         else "",
         strain_id=config["strain_id_field"],
+        divergence_units=config["divergence_units"],
     shell:
         """
         augur refine \
@@ -263,6 +263,7 @@ rule refine:
             --coalescent {params.coalescent} \
             --date-inference {params.date_inference} \
             --date-confidence \
+            --divergence-units {params.divergence_units} \
             --clock-filter-iqd {params.clock_filter_iqd}
         """
 

From 4c7fddd2bee6e5d8496a9d73fb0d2e708eff3aa3 Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Sat, 20 Jan 2024 20:20:45 +0100
Subject: [PATCH 2/2] fix:  add divergence_units also to ci profile

---
 phylogenetic/profiles/ci/builds.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/phylogenetic/profiles/ci/builds.yaml b/phylogenetic/profiles/ci/builds.yaml
index 8ab51370..08dd36c8 100644
--- a/phylogenetic/profiles/ci/builds.yaml
+++ b/phylogenetic/profiles/ci/builds.yaml
@@ -73,6 +73,7 @@ timetree: true
 root: "MK783032 MK783030"
 clock_rate: 5.7e-5
 clock_std_dev: 2e-5
+divergence_units: "mutations"
 
 ## recency
 recency: true