Fast5 file `vbz` problem

[peiyihe]

Hi, Sam,

I'm trying to map a fast5 file with UNCALLED, it seems I need vbz for this file? Is there anything wrong?

pyhe@PYHE_VM:~/UNCALLED/test_for_cam$ uncalled map index/example_ref fast5_filename.txt
Loading fast5s
Mapping
HDF5-DIAG: Error detected in HDF5 (1.8.21) thread 140581483063104:
  #000: H5Dio.c line 223 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: H5Dio.c line 605 in H5D__read(): can't read data
    major: Dataset
    minor: Read failed
  #002: H5Dchunk.c line 2093 in H5D__chunk_read(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #003: H5Dchunk.c line 3123 in H5D__chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #004: H5Z.c line 1311 in H5Z_pipeline(): required filter 'vbz' is not registered
    major: Data filters
    minor: Read failed
  #005: H5PL.c line 380 in H5PL_load(): search in paths failed
    major: Plugin for dynamically loaded library
    minor: Can't get value
  #006: H5PL.c line 738 in H5PL__find(): can't open directory: /usr/local/hdf5/lib/plugin
    major: Plugin for dynamically loaded library
    minor: Can't open directory or file
Traceback (most recent call last):
  File "/home/pyhe/.local/bin/uncalled", line 341, in <module>
    map_cmd(conf, args)
  File "/home/pyhe/.local/bin/uncalled", line 157, in map_cmd
    for p in mapper.update():
RuntimeError: /read_0006a106-77eb-4752-b405-38d1635718fa/Raw/Signal: error in H5Dread
terminate called without an active exception
Aborted (core dumped)
pyhe@PYHE_VM:~/UNCALLED/test_for_cam$ pip install ont-vbz-hdf-plugin

[skovaka]

VBZ is a compression plugin which sometimes must be manually installed: https://github.com/nanoporetech/vbz_compression If you have any trouble see this previous issue for possible solutions: https://github.com/skovaka/UNCALLED/issues/38

[peiyihe]

Thanks! I am successful now.