Issue opening h5 file

[lucygarner]

Hi,

I am getting an error that suggests a problem with my .h5 file, but I am not sure what this is.

demuxEM -p 1 --generate-diagnostic-plots data/raw_feature_h5_matrices/merged/BL1A.h5 results/BL1A_hashtag_counts.csv BLA_demux

My .h5 file was generated by combining multiple raw_feature_bc_matrix.h5 files from Cell Ranger multi. These were merged using mergeH5 from rliger (https://github.com/welch-lab/liger). I had to merge multiple files since I am demultiplexing multiple 10x channels together (all containing the exact same sample).

ERROR:

Traceback (most recent call last):
  File "/Users/lucy/conda/envs/test/bin/demuxEM", line 8, in <module>
    sys.exit(main())
  File "/Users/lucy/conda/envs/test/lib/python3.10/site-packages/demuxEM/__main__.py", line 9, in main
    command.execute()
  File "/Users/lucy/conda/envs/test/lib/python3.10/site-packages/demuxEM/commands/DemuxEM.py", line 61, in execute
    run_pipeline(
  File "/Users/lucy/conda/envs/test/lib/python3.10/site-packages/demuxEM/pipeline/pipeline.py", line 13, in run_pipeline
    data = io.read_input(input_rna_file, genome=kwargs["genome"], modality="rna")
  File "/Users/lucy/conda/envs/test/lib/python3.10/site-packages/pegasusio/decorators.py", line 12, in wrapper_timer
    result = func(*args, **kwargs)
  File "/Users/lucy/conda/envs/test/lib/python3.10/site-packages/pegasusio/readwrite.py", line 161, in read_input
    data = load_10x_h5_file(input_file)
  File "/Users/lucy/conda/envs/test/lib/python3.10/site-packages/pegasusio/hdf5_utils.py", line 165, in load_10x_h5_file
    data = load_file(h5_in)
  File "/Users/lucy/conda/envs/test/lib/python3.10/site-packages/pegasusio/hdf5_utils.py", line 82, in load_10x_h5_file_v3
    M, N = h5_in["matrix/shape"][...]
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/Users/lucy/conda/envs/test/lib/python3.10/site-packages/h5py/_hl/group.py", line 328, in __getitem__
    oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5o.pyx", line 190, in h5py.h5o.open
KeyError: "Unable to open object (object 'shape' doesn't exist)"

Best wishes,
Lucy