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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Issue with Read10X_h5 #6766

Closed zvan14 closed 1 year ago

zvan14 commented 1 year ago

I have used this function before on a mac and I had no issues, but when using windows I can't get the function to work. I am not sure if it has to do with the fact that I am using windows, but I am at a lost on what to do. I have tried moving the file around and copying its path, but I kept getting this issue. I also have left out the C: but the function still will not go through.

RL2103 <-Read10X_h5("C:/Herring_Project/Herring_Files/RL2103_ga22_snRNAseq_raw_matrix.h5.gz", use.names = TRUE, unique.features = TRUE) Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : HDF5-API Errors: error #000: D:/a/rtools-packages/rtools-packages/mingw-w64-hdf5/src/hdf5-1.8.16/src/H5F.c in H5Fopen(): line 604: unable to open file class: HDF5 major: File accessibilty minor: Unable to open file

error #001: D:/a/rtools-packages/rtools-packages/mingw-w64-hdf5/src/hdf5-1.8.16/src/H5Fint.c in H5F_open(): line 1087: unable to read superblock
    class: HDF5
    major: File accessibilty
    minor: Read failed

error #002: D:/a/rtools-packages/rtools-packages/mingw-w64-hdf5/src/hdf5-1.8.16/src/H5Fsuper.c in H5F_super_read(): line 277: file signature not found
    class: HDF5
    major: File accessibilty
    minor: Not an HDF5 file
mojaveazure commented 1 year ago

This is a gzipped HDF5 file, which hdf5r on Windows cannot natively handle. Try ungzipping it before reading it in