From 7d0a4051a3293aaf6247d0c63794fbab5eaf7d9d Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Tue, 19 Nov 2024 03:54:05 -0800 Subject: [PATCH] Adjust raxml to speed up tree building Currently tree building for the global tree took ~4 hours (4:35:46). GitHub Actions has a 6hour runtime limit. Changing some of the parameters with the goal of speeding up tree building without losing quality of trees. Testing: 1. `-f b` to `-f a` to use rapid bootstrapping 2. Use `-N 100` to set the number of bootstraps to 100 3. Use `-x 12345` to set the random seed for bootstrapping 4. Add `-i auto` to automatically determine the best starting tree --- phylogenetic/rules/construct_phylogeny.smk | 3 +++ 1 file changed, 3 insertions(+) diff --git a/phylogenetic/rules/construct_phylogeny.smk b/phylogenetic/rules/construct_phylogeny.smk index 60da9a2..1e6c489 100644 --- a/phylogenetic/rules/construct_phylogeny.smk +++ b/phylogenetic/rules/construct_phylogeny.smk @@ -30,12 +30,15 @@ rule tree: benchmark: "benchmarks/tree.txt" threads: workflow.cores + params: + raxml_tree_builder_args="-f a -m GTRCAT -p 235813 -x 12345 -N 100 -i auto" shell: """ augur tree \ --alignment {input.alignment} \ --output {output.tree} \ --method raxml \ + --tree-builder-args {params.raxml_tree_builder_args:q} \ --nthreads {threads:q} 2>&1 | tee {log} """