OSerror

Problems encountered on 26/09/2022

Problem Situation

When I tried to run baseLess, an error occured：

Traceback (most recent call last):
  File "/home/zxy/anaconda3/envs/baseLess/bin/baseLess", line 11, in <module>
    sys.exit(main())
  File "/home/zxy/anaconda3/envs/baseLess/lib/python3.10/site-packages/baseLess/__main__.py", line 55, in main
    args.func(args)
  File "/home/zxy/anaconda3/envs/baseLess/lib/python3.10/site-packages/baseLess/db_building/build_db.py", line 44, in main
    tr = TrainingRead(f, normalization=args.normalization,
  File "/home/zxy/anaconda3/envs/baseLess/lib/python3.10/site-packages/baseLess/db_building/TrainingRead.py", line 74, in __init__
    self.raw = None
  File "/home/zxy/anaconda3/envs/baseLess/lib/python3.10/site-packages/baseLess/db_building/TrainingRead.py", line 163, in raw
    raw = self.hdf[f'Raw/Reads/{raw_varname}/Signal'][()]
  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 "/home/zxy/anaconda3/envs/baseLess/lib/python3.10/site-packages/h5py/_hl/dataset.py", line 710, in __getitem__
    return self._fast_reader.read(args)
  File "h5py/_selector.pyx", line 366, in h5py._selector.Reader.read
OSError: Can't read data (can't open directory: /home/zxy/anaconda3/envs/baseLess/lib/hdf5/plugin)

Install hdfplugin with commandconda install ont_vbz_hdf_plugin

But an error：

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - ont_vbz_hdf_plugin

Current channels:

  - https://mirrors.sustech.edu.cn/anaconda/pkgs/main/linux-64
  - https://mirrors.sustech.edu.cn/anaconda/pkgs/main/noarch
  - https://mirrors.sustech.edu.cn/anaconda/pkgs/free/linux-64
  - https://mirrors.sustech.edu.cn/anaconda/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Final solution

With this command conda install -c bioconda ont_vbz_hdf_plugin

Details:

(baseLess) zxy@biolab-HP-Z8-G4-Workstation:~$ conda install -c bioconda ont_vbz_hdf_plugin
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 4.14.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/zxy/anaconda3/envs/baseLess

  added / updated specs:
    - ont_vbz_hdf_plugin


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ont_vbz_hdf_plugin-1.0.1   |       hb6da537_3         1.3 MB  bioconda
    ------------------------------------------------------------
                                           Total:         1.3 MB

The following NEW packages will be INSTALLED:

  ont_vbz_hdf_plugin bioconda/linux-64::ont_vbz_hdf_plugin-1.0.1-hb6da537_3

The following packages will be SUPERSEDED by a higher-priority channel:

  openssl            conda-forge::openssl-1.1.1q-h166bdaf_0 --> anaconda/pkgs/main::openssl-1.1.1q-h7f8727e_0


Proceed ([y]/n)? y


Downloading and Extracting Packages
ont_vbz_hdf_plugin-1 | 1.3 MB    | ##################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done