Pharokka Error

Question

[NIkita]

Hi there! Im trying to annotate the viral genom

My input:

pharokka.py -i ./scaffolds.fasta -o ../first_annotated -d /home/nikita/Documents/test_task/pharokkadatabase/

My output:

/home/nikita/.conda/envs/pharokkaENV/lib/python3.10/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])
/home/nikita/.conda/envs/pharokkaENV/lib/python3.10/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)
/home/nikita/.conda/envs/pharokkaENV/lib/python3.10/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])
/home/nikita/.conda/envs/pharokkaENV/lib/python3.10/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)
2025-06-22 18:11:47.066 | INFO     | input_commands:instantiate_dirs:190 - Removing output directory ../first_annotated as -f or --force was specified.
2025-06-22 18:11:47.074 | INFO     | __main__:main:95 - Starting Pharokka v1.7.5
2025-06-22 18:11:47.074 | INFO     | __main__:main:96 - Command executed: Namespace(infile='./scaffolds.fasta', outdir='../first_annotated', database='/home/nikita/Documents/test_task/pharokkadatabase/', threads='1', force=True, prefix='Default', locustag='Default', gene_predictor='default', meta=False, split=False, coding_table='11', evalue='1E-05', fast=False, mmseqs2_only=False, meta_hmm=False, dnaapler=False, custom_hmm='', genbank=False, terminase=False, terminase_strand='nothing', terminase_start='nothing', skip_extra_annotations=False, skip_mash=False, minced_args='', mash_distance=0.2, trna_scan_model='general', citation=False)
2025-06-22 18:11:47.074 | INFO     | __main__:main:97 - Repository homepage is https://github.com/gbouras13/pharokka
2025-06-22 18:11:47.074 | INFO     | __main__:main:98 - Written by George Bouras: [e-mail]
2025-06-22 18:11:47.075 | INFO     | __main__:main:100 - Checking database installation in /home/nikita/Documents/test_task/pharokkadatabase/.
2025-06-22 18:11:47.075 | INFO     | __main__:main:103 - All databases have been successfully checked.
2025-06-22 18:11:47.075 | INFO     | __main__:main:119 - Checking dependencies.
Traceback (most recent call last):
  File "/home/nikita/.conda/envs/pharokkaENV/bin/pharokka.py", line 489, in <module>
    main()
  File "/home/nikita/.conda/envs/pharokkaENV/bin/pharokka.py", line 128, in main
    ) = check_dependencies(args.skip_mash)
  File "/home/nikita/.conda/envs/pharokkaENV/bin/input_commands.py", line 386, in check_dependencies
    phanotate_major_version = int(phanotate_version.split(".")[0])
ValueError: invalid literal for int() with base 10: '/home/nikita/'

i really dont know what should i do i already have tried to reinstall conda env, pharokka and its database

please, help for beginner bioinformatic! :0

Answer 1

[Mensur Dlakic]

Your problem seems to be with phanotate version. Generally speaking, that will be best resolved if you directly communicate with the author on GitHub. This may help:

https://github.com/gbouras13/pharokka/issues/332