issue with read10x_h5 function in seurat

[zvan14]

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 #1: 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 #2: 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 fileI 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 #1: 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 #2: 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

[heteyszabolcs]

Could you solve it somehow? Same issue on Linux.

[Jyng321]

Hi all,
I had the same issue in Windows. After some research, I figured out that it may be a mistake during the data transfer. So I transferred the output raw data after cellranger again and it worked.
I hope it can help.
Best.