Greetings,

 

Thank you for making the data available for download. I have downloaded some data (https://covid19.cog.sanger.ac.uk/submissions/release1/20200804_NasalSwab_Broad_BCH_UMMC_to_CZI.h5ad), however I have been unable to open it

 

I get errors like this:

 

Warning: Unknown file type: h5ad

Warning: 'assay' not set, setting to 'RNA'

Creating h5Seurat file for version 3.1.5.9900

Adding X as data

Adding X as counts

Error: Cannot find feature names in this H5AD file

Execution halted

 

Or this:

 

error #001: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dio.c in H5D__read(): line 551: can't read data

    class: HDF5

    major: Dataset

    minor: Read failed

 

error #002: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dchunk.c in H5D__chunk_read(): line 1875: unable to read raw data chunk

    class: HDF5

    major: Low-level I/O

    minor: Read failed

 

error #003: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dchunk.c in H5D__chunk_lock(): line 2905: data pipeline read failed

    class: HDF5

    major: Data filters

    minor: Filter operation failed

 

error #004: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Z.c in H5Z_pipeline(): line 1347: required filter 'lzf' is not registered

   class: HDF5

    major: Data filters

    minor: Read failed

 

There are many message boards that have listed possible solutions, but I have not been able to get any of them to work. Could you provide some guidance as to what programs are used to open/manipulate these files please?

 

Sincerely,

 

Erin