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。

.envrc

@@ -2,7 +2,6 @@ set +u
 export PROJECTHOME="/home/ywtang/project/biyelunwen"
 export SCRIPTS="$PROJECTHOME/99.scripts"
 export PUEUE_CONFIG_PATH="$PROJECTHOME/.pueue.yml"
-watch_file pixi.lock 
+watch_file pixi.lock
 eval "$(pixi shell-hook)"
 PATH_add $SCRIPTS/bucky/bin
-PATH_add $SCRIPTS/ticr

99.scripts/miscs/bucky.pl

@@ -1452,16 +1452,16 @@ sub check_bucky_version {
 	die "  Error determining BUCKy version.\n" if (!@version_parts);
 
 	# Check that version is >= 1.4.4
-	if (defined($version_parts[0]) && $version_parts[0] > 1) {
+	if (defined($version_parts[0]) && int($version_parts[0]) > 1) {
 		print "  BUCKy version check passed.\n";
 		return;
 	}
-	elsif ((defined($version_parts[0]) && $version_parts[0] == 1) && (defined($version_parts[1]) && $version_parts[1] > 4)) {
+	elsif ((defined($version_parts[0]) && int($version_parts[0]) == 1) && (defined($version_parts[1]) && int($version_parts[1]) > 4)) {
 		print "  BUCKy version check passed.\n";
 		return;
 	}
-	elsif (((defined($version_parts[0]) && $version_parts[0] == 1) && (defined($version_parts[1]) && $version_parts[1] == 4))
+	elsif (((defined($version_parts[0]) && int($version_parts[0]) == 1) && (defined($version_parts[1]) && int($version_parts[1]) == 4))
-		  && defined($version_parts[2]) && $version_parts[2] >= 4) {
+		  && defined($version_parts[2]) && int($version_parts[2]) >= 4) {
 		print "  BUCKy version check passed.\n";
 		return;
 	}

99.scripts/miscs/raxml.sh

@@ -16,5 +16,5 @@ mkdir -p "$outdir"
 modeltest-ng -p "$threads" -r 12345 --force -i "$aln" -d nt -t ml -o "$out".modeltest
 # run raxml-ng
 cmd=$(grep "raxml-ng" "$out".modeltest.out | tail -n 1 | sed 's/> //')
-params="--all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
+params="--blopt nr_safe --all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
 bash -c "$cmd $params" >/dev/null

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);

pixi.lock

@@ -153,6 +153,8 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/ca-certificates-2025.11.12-hbd8a1cb_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/cairo-1.18.4-h3394656_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cairocffi-1.7.1-pyhd8ed1ab_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cairosvg-2.8.2-pyhd8ed1ab_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/cd-hit-4.8.1-h5ca1c30_13.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/cdbtools-0.99-h077b44d_12.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/certifi-2025.11.12-pyhd8ed1ab_0.conda
@@ -168,11 +170,13 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/coreutils-9.5-hd590300_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/cpp-expected-1.3.1-h171cf75_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cpython-3.11.14-py311hd8ed1ab_2.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cssselect2-0.8.0-pyhd8ed1ab_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/curl-8.17.0-h4e3cde8_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/cyrus-sasl-2.1.28-hd9c7081_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/dav1d-1.2.1-hd590300_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/dbus-1.16.2-h3c4dab8_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/dendropy-5.0.8-pyhdfd78af_1.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/diamond-2.1.16-h13889ed_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/distro-1.9.0-pyhd8ed1ab_1.conda
@@ -737,6 +741,7 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/tbb-devel-2022.3.0-h74b38a2_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/td2-1.0.6-pyhdfd78af_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/threadpoolctl-3.6.0-pyhecae5ae_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/tinycss2-1.5.1-pyhcf101f3_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/tktable-2.10-h8d826fa_7.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/toml-0.10.2-pyhd8ed1ab_2.conda
@@ -761,6 +766,7 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/unicodedata2-17.0.0-py311h49ec1c0_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/urllib3-2.5.0-pyhd8ed1ab_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/wayland-1.24.0-hd6090a7_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_3.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/wget-1.21.4-hda4d442_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/x265-3.5-h924138e_3.tar.bz2
@@ -1950,6 +1956,31 @@ packages:
   license: LGPL-2.1-only or MPL-1.1
   size: 978114
   timestamp: 1741554591855
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cairocffi-1.7.1-pyhd8ed1ab_1.conda
+  sha256: 1f9642b94454fbcb605f5c711c512cea2147246a4e23aa9baddbda5324089c78
+  md5: 54b7517cb759be8279efe23708528fe5
+  depends:
+  - cairo >=1.14
+  - cffi >=1.1
+  - python >=3.9
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 67048
+  timestamp: 1735230077496
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cairosvg-2.8.2-pyhd8ed1ab_0.conda
+  sha256: 7c76dfe182f775ac9b0a92668fdf5a1d8db6b1459b9ac971d90fcb33609294cf
+  md5: a873c27598843c20dbb200681f49ea96
+  depends:
+  - cairocffi
+  - cssselect2
+  - defusedxml
+  - pillow
+  - python >=3.9
+  - tinycss2
+  license: LGPL-3.0-only
+  license_family: LGPL
+  size: 44459
+  timestamp: 1747337159019
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/cd-hit-4.8.1-h5ca1c30_13.tar.bz2
   sha256: 8793a98a7c93b9ade5caaa85e6eeccec69d774c197b772a8132373de2d6ce8e1
   md5: 8b5beac305bcf38b77be27e0233e4076
@@ -2132,6 +2163,17 @@ packages:
   license: Python-2.0
   size: 47257
   timestamp: 1761172995774
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/cssselect2-0.8.0-pyhd8ed1ab_0.conda
+  sha256: 0a6728d77e337fd5b543765b0cd05eda996b63f4ef0c1bb34a02d78a7d123a68
+  md5: 504bf822bea0f84547fb31e41de19714
+  depends:
+  - python >=3.9
+  - tinycss2
+  - webencodings
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 20425
+  timestamp: 1751498485591
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/curl-8.17.0-h4e3cde8_0.conda
   sha256: 3fb39c401fbdbaf68b8f25c1d81600d2a771b6467cc5d7c88fbd1e06d8825ee1
   md5: a37bd62e2c34797cdb577920b35f3bc5
@@ -2196,6 +2238,15 @@ packages:
   license_family: GPL
   size: 437860
   timestamp: 1747855126005
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2
+  sha256: 9717a059677553562a8f38ff07f3b9f61727bd614f505658b0a5ecbcf8df89be
+  md5: 961b3a227b437d82ad7054484cfa71b2
+  depends:
+  - python >=3.6
+  license: PSF-2.0
+  license_family: PSF
+  size: 24062
+  timestamp: 1615232388757
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/dendropy-5.0.8-pyhdfd78af_1.tar.bz2
   sha256: 102790b465893f5a5c4c3fa045f677e23f990ecc6d1b61d240153c3569a5b99f
   md5: 0fa94922431d1074792639704d19461d
@@ -9579,6 +9630,17 @@ packages:
   license_family: BSD
   size: 23869
   timestamp: 1741878358548
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/tinycss2-1.5.1-pyhcf101f3_0.conda
+  sha256: 7c803480dbfb8b536b9bf6287fa2aa0a4f970f8c09075694174eb4550a4524cd
+  md5: c0d0b883e97906f7524e2aac94be0e0d
+  depends:
+  - python >=3.10
+  - webencodings >=0.4
+  - python
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 30571
+  timestamp: 1764621508086
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda
   sha256: 1544760538a40bcd8ace2b1d8ebe3eb5807ac268641f8acdc18c69c5ebfeaf64
   md5: 86bc20552bf46075e3d92b67f089172d
@@ -9905,6 +9967,15 @@ packages:
   license_family: MIT
   size: 329779
   timestamp: 1761174273487
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_3.conda
+  sha256: 19ff205e138bb056a46f9e3839935a2e60bd1cf01c8241a5e172a422fed4f9c6
+  md5: 2841eb5bfc75ce15e9a0054b98dcd64d
+  depends:
+  - python >=3.9
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 15496
+  timestamp: 1733236131358
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/wget-1.21.4-hda4d442_0.conda
   sha256: 70df4ac8cca488618458af4705706551cef7e402bac9c2c41dd17148f60cbd1f
   md5: 361e96b664eac64a33c20dfd11affbff

pixi.toml

@@ -51,6 +51,7 @@ mmseqs2 = ">=18.8cc5c,<19"
 paml = ">=4.10.9,<5"
 beagle-lib = "==3.1.2"
 mrbayes = ">=3.2.7,<4"
+cairosvg = ">=2.8.2,<3"
 
 [feature.beast.dependencies]
 beagle-lib = ">=4.0.1,<5"