无法安装Bioconductor的ShortRead包，求fastq.gz转fasta解决方案

问题背景 #

在R 4.1.1（对应Bioconductor 3.14）环境中，尝试安装并加载ShortRead包以使用readFastq函数时，遭遇多类错误，无法正常完成操作，需排查故障或寻求更简便的fastq.gz转fasta方法。

错误信息 #

1. 包加载失败 #

> library(ShortRead)
Error in library(Shortread) : there is no package called 'ShortRead'

2. 依赖包编译失败（核心错误） #

ln: failed to create symbolic link 'libhts.so.2': Operation not supported
make: *** [Makevars:28: populate-usrlib-dir] Error 1
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/Rhtslib’
ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/Rsamtools’
ERROR: dependency ‘Rsamtools’ is not available for package ‘GenomicAlignments’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/GenomicAlignments’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’, ‘Rhtslib’ are not available for package ‘ShortRead’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/ShortRead’

3. textshaping/ragg包配置失败 #

ERROR: configuration failed for package ‘textshaping’
* removing ‘/opt/conda/envs/r/lib/R/library/textshaping’
* restoring previous ‘/opt/conda/envs/r/lib/R/library/textshaping’
* installing *source* package ‘ragg’ ...
** package ‘ragg’ successfully unpacked and MD5 sums checked
** using staged installation

ERROR: configuration failed for package ‘ragg’
* removing ‘/opt/conda/envs/r/lib/R/library/ragg’
* restoring previous ‘/opt/conda/envs/r/lib/R/library/ragg’

The downloaded source packages are in
    ‘/tmp/RtmpgByRyT/downloaded_packages’ 

已执行的安装命令 #

#Installing ShortRead package containing the readFastq function
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(version="3.14")
BiocManager::install("GenomeInfoDbData")
BiocManager::install("GenomeInfoDb")
BiocManager::install("ShortRead")


#Loading the library
library(ShortRead)

当前会话信息 #

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS/LAPACK: /opt/conda/envs/r/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base      

other attached packages:
[1] BiocManager_1.30.19

loaded via a namespace (and not attached):
 [1] compiler_4.1.1  fastmap_1.1.0   cli_3.4.1       htmltools_0.5.3 tools_4.1.1    
 [6] rstudioapi_0.14 yaml_2.3.6      rmarkdown_2.17  knitr_1.40      xfun_0.34      
[11] digest_0.6.30   rlang_1.0.6     evaluate_0.17 

故障排查建议 #

1. 解决Rhtslib编译失败问题（核心） #

错误提示ln: failed to create symbolic link 'libhts.so.2': Operation not supported，通常因安装目录无软链接权限或文件系统不支持软链接导致：

• 切换可写安装目录：修改R包安装路径到本地有完整权限的目录，再重新安装：

  .libPaths(c("/home/jovyan/R/libs", .libPaths()))
  BiocManager::install("ShortRead")
  

• 用conda安装预编译包：conda环境下直接安装二进制包，跳过源码编译：

  conda install -c bioconda bioconductor-shortread
  

• 手动修改Rhtslib源码：下载对应版本的Rhtslib源码包，将Makevars文件中的ln -s命令替换为cp（复制文件替代软链接），再本地安装：

  install.packages("path/to/Rhtslib.tar.gz", repos = NULL, type = "source")
  

2. 解决textshaping/ragg配置失败问题 #

这两个包依赖系统图形库，conda环境下直接用conda安装：

conda install -c conda-forge r-textshaping r-ragg

3. 验证Bioconductor版本匹配 #

确认当前Bioconductor版本为3.14，若不匹配则更新并重启R：

BiocManager::install(version = "3.14", update = TRUE, ask = FALSE)

替代方案：fastq.gz转fasta #

若不想安装ShortRead，可选用以下更简便的方法：

1. Linux命令行工具（最快） #

直接用zcat+awk处理压缩文件，无需启动R：

zcat input.fastq.gz | awk 'NR%4==1{print ">"substr($0,2)}NR%4==2{print}' > output.fasta

解释：提取fastq文件的第1行（替换@为>作为fasta标题）和第2行（序列内容）

2. R基础包实现 #

无需额外安装包，用R基础函数完成转换：

# 读取压缩的fastq文件
fastq_lines <- readLines(gzfile("input.fastq.gz"))
# 提取fasta格式的行
fasta_lines <- c(
  paste0(">", substr(fastq_lines[seq(1, length(fastq_lines), 4)], 2)),
  fastq_lines[seq(2, length(fastq_lines), 4)]
)
# 写入fasta文件
writeLines(fasta_lines, "output.fasta")

内容的提问来源于stack exchange，提问作者Anna Keisha Boateng