使用Tax4Fun2包runRefBlast()函数时文件找不到错误求助

环境信息 #

• 系统：Ubuntu 16.0
• R版本：4.1.1
• 涉及包：Tax4Fun2

执行的代码 #

终端命令 #

export PATH=$PATH:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/blast_bin/bin/
R

R代码 #

PATH = "media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/blast_bin/bin/"
runRefBlast(path_to_otus = "media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/fasta",
path_to_reference_data = PATH,
path_to_temp_folder = "media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Ref100NR",
database_mode = "Ref100NR",
use_force = T, num_threads = 4)

报错信息 #

chmod: can't access to '/home/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2//blast_bin/bin/blastn': It doesn't exist the file or directory
sh: 1: /home/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2//blast_bin/bin/blastn: not found
Error in system(command = paste(blast_bin, "-help"), intern = T) :
error in running command

解决建议 #

• 修正路径格式：R代码中所有路径开头缺少/，导致被解析为当前用户目录（/home/juanm/）下的相对路径，全部改为绝对路径：

  PATH = "/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/blast_bin/bin/"
  runRefBlast(path_to_otus = "/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/fasta",
  path_to_reference_data = PATH,
  path_to_temp_folder = "/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Ref100NR",
  database_mode = "Ref100NR",
  use_force = T, num_threads = 4)
  

• 验证blastn文件存在性：在终端执行以下命令，确认blastn工具是否存在：

  ls /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/blast_bin/bin/blastn
  

  如果返回文件不存在，需重新下载完整的Tax4Fun2参考数据包，确保blast工具组件完整。
• 添加可执行权限：即使文件夹有root权限，也要确保blastn本身具备可执行权限，执行：

  sudo chmod +x /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/blast_bin/bin/blastn
  

• 测试blastn可用性：在终端直接运行blastn测试是否能正常工作：

  /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d2/Tax4Fun2/R/Tax4Fun2_ReferenceData_v2/blast_bin/bin/blastn -help
  

  若能输出帮助信息，说明blast工具正常，再重新运行R中的代码。

内容的提问来源于stack exchange，提问作者Juan Manuel Luque