Linux R语言打开.h5文件异常
2022-06-10 本文已影响0人
倪桦
6月10日从GEO数据库下载了作者上传的表达矩阵h5格式文件，需用从中提取出表达矩阵然后重构Seurat分析对象；该exp_matrix.hdf5文件在我的Window系统上，可以通过rhdf5::H5Fopen和hdf5r::H5File$new两种方法打开读取文件内容。但是由于文件太大，有6个G，在我24G内存的Windows系统上没办法完全加载出矩阵。于是就把文件上传到服务器集群进行处理，以同样的方式尝试打开exp_matrix.hdf5文件，碰到了以下问题：
- 1.
rhdf5::H5Fopen函数打开error：
data.h5 <- H5Fopen(name = "exp_matrix.hdf5")
Error in H5Fopen(name = "exp_matrix.hdf5", :
HDF5. File accessibility. Unable to open file.
- 2.
hdf5r::H5File$new函数打开error：
hdf5r::H5File$new("exp_matrix.hdf5", mode="r")
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) :
HDF5-API Errors:
error #000: H5F.c in H5Fopen(): line 620: unable to open file
class: HDF5
major: File accessibility
minor: Unable to open file
error #001: H5VLcallback.c in H5VL_file_open(): line 3501: failed to iterate over available VOL connector plugins
class: HDF5
major: Virtual Object Layer
minor: Iteration failed
error #002: H5PLpath.c in H5PL__path_table_iterate(): line 578: can't iterate over plugins in plugin path '(null)'
class: HDF5
major: Plugin for dynamically loaded library
minor: Iteration failed
error #003: H5PLpath.c in H5PL__path_table_iterate_process_path(): line 620: can't open directory: ~/local/Minconda/envs/scRNA/lib/hdf5/plugin
class: HDF5
major: Plugin for dynamically loaded library
minor: Can't open directory or file
error #004: H5VLcallback.c in H5VL__file_open(): line 3351: open faile
解决方案：编辑Linux用户的配置文件(.bashrc)添加以下两句环境变量：
export HDF5_USE_FILE_LOCKING="FALSE"
export RHDF5_USE_FILE_LOCKING="FALSE"
