更新脚本和配置，修复 BUCKy 版本检查逻辑，调整 RAxML 脚本参数，增加 cairosvg 依赖，并更新 pixi.lock 文件以反映新依赖。

99.scripts/workflow/phylogeny_reconstruction/03.run_raxml.sh

@@ -1,7 +1,7 @@
 #! /bin/bash
 set -e
 SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
-THREADS=${THREADS:-4}
+THREADS=${THREADS:-3}
 
 if [ "$#" -ne 3 ]; then
     echo "Usage: $0 <in_dir> <out_dir> <ext>"

99.scripts/workflow/phylogeny_reconstruction/03.snaq.jl

@@ -13,13 +13,13 @@
 # Running SNaQ Analysis
 using PhyloNetworks, SNaQ;
 using Distributed;
-addprocs(5);
+addprocs(9);
 @everywhere using PhyloNetworks, SNaQ;
 nruns = 100; # number of runs for each hmax
-astralfile = joinpath("..", "..", "species_tree", "aster.out");
+astralfile = joinpath("..", "species_tree", "coal.tre");
 astraltree = readnewick(astralfile);
 
-### Reading RAxML gene trees and ASTRAL species tree 
+### Reading RAxML gene trees and ASTRAL species tree
 ### running in raxml_snaq/ folder
 # raxmltrees = joinpath("..", "..", "species_tree", "all.trees");
 # inputCF = readtrees2CF(raxmltrees);
@@ -31,7 +31,7 @@ astraltree = readnewick(astralfile);
 
 ### Alternatively, reading in the input files from Bucky
 ### running in input_snaq/ folder
-inputCFfile = joinpath("bucky_1.CFs.csv");
+inputCFfile = joinpath("..","bucky","bucky_1","input.mb.CFs.csv");
 inputCF = readtableCF(inputCFfile);
 net0 = snaq!(astraltree, inputCF, hmax=0, filename="net0", seed=123, outgroup="Zju", runs=nruns);
 net1 = snaq!(net0, inputCF, hmax=1, filename="net1", seed=123, outgroup="Zju", runs=nruns);