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random_base() issue #2

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JiaGengChang opened this issue Aug 14, 2022 · 1 comment
Open

random_base() issue #2

JiaGengChang opened this issue Aug 14, 2022 · 1 comment

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@JiaGengChang
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I get the following error with the function random_base in virnatrap.py:
random_base() takes 0 positional arguments but 1 were given.

I replaced the call to random_base with random.choice(NUCLEOTIDES), rebuilt the package, and it fixed the issue.

This issue does not appear with the example file given. However, it appears with large files (maybe something to do with multiprocessing).

@JiaGengChang
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Contents of my environment

name: virnatrap
channels:
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - ca-certificates=2022.6.15=ha878542_0
  - ld_impl_linux-64=2.36.1=hea4e1c9_2
  - libffi=3.4.2=h7f98852_5
  - libgcc-ng=12.1.0=h8d9b700_16
  - libgomp=12.1.0=h8d9b700_16
  - libnsl=2.0.0=h7f98852_0
  - libsqlite=3.39.2=h753d276_1
  - libstdcxx-ng=12.1.0=ha89aaad_16
  - libzlib=1.2.12=h166bdaf_2
  - ncurses=6.3=h27087fc_1
  - openssl=3.0.5=h166bdaf_1
  - pip=22.2.2=pyhd8ed1ab_0
  - python=3.7.12=hf930737_100_cpython
  - python_abi=3.7=2_cp37m
  - readline=8.1.2=h0f457ee_0
  - setuptools=64.0.3=py37h89c1867_0
  - sqlite=3.39.2=h4ff8645_1
  - tk=8.6.12=h27826a3_0
  - wheel=0.37.1=pyhd8ed1ab_0
  - xz=5.2.6=h166bdaf_0
  - pip:
    - absl-py==1.2.0
    - argparse==1.4.0
    - astunparse==1.6.3
    - cachetools==5.2.0
    - certifi==2022.6.15
    - charset-normalizer==2.1.0
    - flatbuffers==1.12
    - gast==0.4.0
    - google-auth==2.10.0
    - google-auth-oauthlib==0.4.6
    - google-pasta==0.2.0
    - grpcio==1.47.0
    - h5py==3.7.0
    - idna==3.3
    - importlib-metadata==4.12.0
    - keras==2.9.0
    - keras-preprocessing==1.1.2
    - libclang==14.0.6
    - markdown==3.4.1
    - markupsafe==2.1.1
    - numpy==1.21.6
    - oauthlib==3.2.0
    - opt-einsum==3.3.0
    - packaging==21.3
    - protobuf==3.19.4
    - pyasn1==0.4.8
    - pyasn1-modules==0.2.8
    - pyparsing==3.0.9
    - requests==2.28.1
    - requests-oauthlib==1.3.1
    - rsa==4.9
    - six==1.16.0
    - tensorboard==2.9.1
    - tensorboard-data-server==0.6.1
    - tensorboard-plugin-wit==1.8.1
    - tensorflow==2.9.1
    - tensorflow-estimator==2.9.0
    - tensorflow-io-gcs-filesystem==0.26.0
    - termcolor==1.1.0
    - typing-extensions==4.3.0
    - urllib3==1.26.11
    - virnatrap==1
    - werkzeug==2.2.2
    - wrapt==1.14.1
    - zipp==3.8.1
prefix: /scratch/deep_learning/jchang6/mambaforge/envs/virnatrap

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