AttributeError when there is no candidate propertied or candidate SHPs

[emkawabat]

Description:

When the pipeline finds no candidate propertied or candidate SHPs, it enters the if-statement to check for the argument ‘chunk’ to skip the current chunk if this option was used. However, it looks like the variable name was supposed to be chunk_size and not chunk.

• Error location: File "launcher.py", line 352

Arguments:

python /home/tools/RRNPP_detector/rrnpp_detector.py --fna "${genome}.fna" -o "$genome_output"

Environment:

Conda Env:

name: rrnpp_env_2022
channels:
  - defaults
  - bioconda
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - blast=2.12.0=hf3cf87c_4
  - bzip2=1.0.8=h4bc722e_7
  - c-ares=1.34.5=hb9d3cd8_0
  - ca-certificates=2025.6.15=hbd8a1cb_0
  - colorama=0.4.6=pyhd8ed1ab_1
  - curl=7.88.1=hdc1c0ab_1
  - dbus=1.13.6=h5008d03_3
  - entrez-direct=24.0=he881be0_0
  - expat=2.7.0=h5888daf_0
  - freetype=2.12.1=h267a509_2
  - glib=2.80.2=hf974151_0
  - glib-tools=2.80.2=hb6ce0ca_0
  - hmmer=3.3.2=hdbdd923_4
  - keyutils=1.6.1=h166bdaf_0
  - krb5=1.20.1=h81ceb04_0
  - ld_impl_linux-64=2.43=h1423503_5
  - libasprintf=0.24.1=h8e693c7_0
  - libblas=3.9.0=31_h59b9bed_openblas
  - libcblas=3.9.0=31_he106b2a_openblas
  - libcurl=7.88.1=hdc1c0ab_1
  - libedit=3.1.20250104=pl5321h7949ede_0
  - libev=4.33=hd590300_2
  - libexpat=2.7.0=h5888daf_0
  - libffi=3.4.6=h2dba641_1
  - libgcc=15.1.0=h767d61c_2
  - libgcc-ng=15.1.0=h69a702a_2
  - libgettextpo=0.24.1=h5888daf_0
  - libgfortran=15.1.0=h69a702a_2
  - libgfortran5=15.1.0=hcea5267_2
  - libglib=2.80.2=hf974151_0
  - libgomp=15.1.0=h767d61c_2
  - libiconv=1.18=h4ce23a2_1
  - libidn2=2.3.8=ha4ef2c3_0
  - liblapack=3.9.0=31_h7ac8fdf_openblas
  - liblzma=5.8.1=hb9d3cd8_2
  - liblzma-devel=5.8.1=hb9d3cd8_2
  - libnghttp2=1.58.0=h47da74e_1
  - libnsl=2.0.1=hd590300_0
  - libopenblas=0.3.29=pthreads_h94d23a6_0
  - libpng=1.6.43=h2797004_0
  - libsqlite=3.46.0=hde9e2c9_0
  - libssh2=1.11.0=h0841786_0
  - libstdcxx=15.1.0=h8f9b012_2
  - libstdcxx-ng=15.1.0=h4852527_2
  - libunistring=0.9.10=h7f98852_0
  - libuuid=2.38.1=h0b41bf4_0
  - libxcb=1.17.0=h8a09558_0
  - libxcrypt=4.4.36=hd590300_1
  - libzlib=1.2.13=h4ab18f5_6
  - ncurses=6.5=h2d0b736_3
  - numpy=1.26.4=py310hb13e2d6_0
  - openjdk=11.0.13=h87a67e3_0
  - openssl=3.5.0=h7b32b05_1
  - orfipy=0.0.4=py310h184ae93_4
  - pandas=1.4.2=py310h769672d_2
  - pcre=8.45=h9c3ff4c_0
  - pcre2=10.43=hcad00b1_0
  - perl=5.32.1=7_hd590300_perl5
  - perl-archive-tar=3.04=pl5321hdfd78af_0
  - perl-carp=1.38=pl5321hdfd78af_4
  - perl-common-sense=3.75=pl5321hdfd78af_0
  - perl-compress-raw-bzip2=2.201=pl5321h87f3376_1
  - perl-compress-raw-zlib=2.105=pl5321h87f3376_0
  - perl-encode=3.19=pl5321hec16e2b_1
  - perl-exporter=5.72=pl5321hdfd78af_2
  - perl-exporter-tiny=1.002002=pl5321hdfd78af_0
  - perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0
  - perl-io-compress=2.201=pl5321h503566f_5
  - perl-io-zlib=1.15=pl5321hdfd78af_0
  - perl-json=4.10=pl5321hdfd78af_1
  - perl-json-xs=4.03=pl5321h9948957_4
  - perl-list-moreutils=0.430=pl5321hdfd78af_0
  - perl-list-moreutils-xs=0.430=pl5321h7b50bb2_5
  - perl-parent=0.236=pl5321hdfd78af_2
  - perl-pathtools=3.75=pl5321hec16e2b_3
  - perl-scalar-list-utils=1.62=pl5321hec16e2b_1
  - perl-types-serialiser=1.01=pl5321hdfd78af_0
  - pip=22.0.4=pyhd8ed1ab_0
  - prodigal=2.6.3=h7b50bb2_10
  - psutil=7.0.0=py310ha75aee5_0
  - pthread-stubs=0.4=hb9d3cd8_1002
  - pyahocorasick=2.1.0=py310ha75aee5_1
  - pyfastx=2.1.0=py310h1af8fb7_3
  - python=3.10.14=hd12c33a_0_cpython
  - python-dateutil=2.9.0.post0=pyhff2d567_1
  - python_abi=3.10=7_cp310
  - pytz=2025.2=pyhd8ed1ab_0
  - readline=8.2=h8c095d6_2
  - setuptools=80.9.0=pyhff2d567_0
  - six=1.17.0=pyhd8ed1ab_0
  - sqlite=3.38.5=h4ff8645_0
  - tk=8.6.13=noxft_h4845f30_101
  - tzdata=2025b=h78e105d_0
  - wget=1.21.4=hda4d442_0
  - wheel=0.45.1=pyhd8ed1ab_1
  - xorg-libxau=1.0.12=hb9d3cd8_0
  - xorg-libxdmcp=1.1.5=hb9d3cd8_0
  - xz=5.8.1=hbcc6ac9_2
  - xz-gpl-tools=5.8.1=hbcc6ac9_2
  - xz-tools=5.8.1=hb9d3cd8_2
  - zlib=1.2.13=h4ab18f5_6
  - zstd=1.5.6=ha6fb4c9_0
  - pip:
      - cython==3.1.2
prefix: /home/.conda/envs/rrnpp_env_2022

Error Message:

  3 potential receptors
* Searching small ORFs with RBS in flanking regions of candidate receptors ...
Traceback (most recent call last):
  File "/home/tools/RRNPP_detector/rrnpp_detector.py", line 73, in <module>
    main()
  File "/home/tools/RRNPP_detector/rrnpp_detector.py", line 69, in main
    launcher(args, parameters, rrnpp_detector_dir, current_dir, out_dir, working_dir, fasta_dir, 
  File "/home/tools/RRNPP_detector/rrnpp_detector/launcher.py", line 352, in launcher
    if args.chunk:
AttributeError: 'Namespace' object has no attribute 'chunk'