hdf5 issue

[GianlucaMattei]

Hello,
After installing nanopolish 0.14.0, after installing hd5plugin with "pip install hdf5plugin" and after running "export HDF5_PLUGIN_PATH=/usr/local/hdf5/lib/plugin" (I do no have this path btw)

I get this error:

/data1/Tools/lib/nanopolish/nanopolish call-methylation -r ${FASTQ}.fastq -b ${SAMPLE}.bam -g hs37d5.decoy.fa -t ${THN} > ${SAMPLE}.methylcalls..tsv
HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 140534143227648:
  #000: H5Dio.c line 173 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: H5Dio.c line 550 in H5D__read(): can't read data
    major: Dataset
    minor: Read failed
  #002: H5Dchunk.c line 1872 in H5D__chunk_read(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #003: H5Dchunk.c line 2902 in H5D__chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #004: H5Z.c line 1357 in H5Z_pipeline(): required filter 'vbz' is not registered
    major: Data filters
    minor: Read failed
  #005: H5PL.c line 298 in H5PL_load(): search in paths failed
    major: Plugin for dynamically loaded library
    minor: Can't get value
  #006: H5PL.c line 402 in H5PL__find(): can't open directory
    major: Plugin for dynamically loaded library
    minor: Can't open directory or file
The fast5 file is compressed with VBZ but the required plugin is not loaded. Please read the instructions here: https://github.com/nanoporetech/vbz_compression/issues/5

How to fix it?
Thanks

[0x55555555]

Hi @GianlucaMattei ,

Have you installed the vbz hdf plugin from this project (from: https://github.com/nanoporetech/vbz_compression/releases/tag/1.0.2)

Thanks,

• George

[GianlucaMattei]

Hi,
thanks for answering
Yes I installed pyvbz-1.0.1-cp36-cp36m-linux_x86_64.whl with pip

[0x55555555]

Hello @GianlucaMattei ,

The wheel provides tools to work with vbz, but does not install the general purpose hdf filter.

You'll need the deb, pkg or msi (depending on platform) from the release page to pull in the hdf plugin.

Thanks,

• George

[GianlucaMattei]

Hi @jorj1988
Thanks for clarification,
now everything works...even if at this point I think I have installed a lot of more things that those needed, so I can not identify the minimum set of tool to install :)
Thanks
Gianluca