Error in if (node.number == (Ntip(tree) + 1)) cat("Note: you chose to re-root the tree at it's current root.\n") : the condition has length > 1

非常抱歉，我之前的回答有误。在使用`root`函数时，我们不能同时指定多个基因树的外群。为了解决这个问题，我们需要对基因树文件进行循环处理，并且每次处理一个基因树文件时，都要重新读取物种树。以下是更新后的代码：

library(ape)
library(tools)

# 设置物种树文件路径
species_tree_file <- "species_tree.treefile"

# 设置基因树目录和输出目录
gene_tree_folder <- "/ifs1/User/dengwei/NTF_data/rotted_gene_tree"
output_folder <- "/ifs1/User/dengwei/NTF_data/adj_gene_tree"

# 定义函数：将基因树转化为有根树并保存到输出目录
convert_to_rooted_tree <- function(gene_tree_file, species_tree, output_folder) {
  # 读取物种树
  species_tree <- read.tree(species_tree)
  
  # 读取基因树
  gene_tree <- read.tree(gene_tree_file)
  
  # 设置外群为物种树的根节点
  outgroup <- species_tree$root$tip.label
  
  # 定根
  rooted_tree <- root(gene_tree, outgroup = outgroup)
  
  # 获取基因树文件名
  gene_tree_file_name <- file_path_sans_ext(basename(gene_tree_file))
  
  # 构建输出文件路径
  output_file <- file.path(output_folder, paste0(gene_tree_file_name, "_rooted.treefile"))
  
  # 保存有根基因树
  write.tree(rooted_tree, file = output_file)
}

# 获取基因树文件列表
gene_tree_files <- list.files(path = gene_tree_folder, pattern = ".treefile", full.names = TRUE)

# 遍历基因树文件并逐个转化为有根基因树
for (gene_tree_file in gene_tree_files) {
  convert_to_rooted_tree(gene_tree_file, species_tree_file, output_folder)
}

请将`species_tree.treefile`替换为你实际的物种树文件路径。然后，设置基因树目录和输出目录的路径。代码中定义了一个名为`convert_to_rooted_tree`的函数，用于将单个基因树转化为有根基因树，并将其保存到输出目录中。最后，通过遍历基因树文件列表，调用`convert_to_rooted_tree`函数逐个处理基因树文件。请确保你已经安装了ape包和tools包。