8000 pyHMMER not running · Issue #383 · gbouras13/pharokka · GitHub
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OlayaRG opened this issue Mar 10, 2025 · 0 comments
Open

pyHMMER not running #383

OlayaRG opened this issue Mar 10, 2025 · 0 comments

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@OlayaRG
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OlayaRG commented Mar 10, 2025 •
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Hi,
I am having issues with pyHMMER. it is not running. and I am getting the following error

 | __main__:main:363 - Running PyHMMER on PHROGs.
Traceback (most recent call last):
  File "/mnt/DATA/home/LMGM/mee/miniconda3/bin/pharokka.py", line 499, in <module>
    main()
  File "/mnt/DATA/home/LMGM/mee/miniconda3/bin/pharokka.py", line 364, in main
    best_results_pyhmmer = run_pyhmmer(
                           ^^^^^^^^^^^^
  File "/mnt/DATA/home/LMGM/mee/miniconda3/bin/hmm.py", line 40, in run_pyhmmer
    protein = hits.query_name.decode()  # get protein from the hit
              ^^^^^^^^^^^^^^^
AttributeError: 'pyhmmer.plan7.TopHits' object has no attribute 'query_name'

I am running with it with pyhmmer 0.11.0 py312h0fa9677_0 bioconda

not sure if it is related, but i also have some warnings at the beginning, but it still runs fine.
/mnt/DATA/home/LMGM/mee/miniconda3/lib/python3.12/site-packages/numpy/_core/getlimits.py:558: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
/mnt/DATA/home/LMGM/mee/miniconda3/lib/python3.12/site-packages/numpy/_core/getlimits.py:90: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  return self._float_to_str(self.smallest_subnormal)
/mnt/DATA/home/LMGM/mee/miniconda3/lib/python3.12/site-packages/numpy/_core/getlimits.py:558: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
/mnt/DATA/home/LMGM/mee/miniconda3/lib/python3.12/site-packages/numpy/_core/getlimits.py:90: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  return self._float_to_str(self.smallest_subnormal)

I saw a similar issue being reported, and i running mash 2.2.2 ha61e061_2 bioconda

thanks for your help,
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