Issues with DeepNOG file not found + PNG

[Siljael]

Hello!

I keep getting this error when trying to run my genome:

There's been an error finding cairoSVG library, so PNG images might be different from expected. Please prefer using SVG output.
/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
  "Premature end of file in sequence data", BiopythonParserWarning

GBK file transformed into faa succesfully. File saved as genovi-temp/contig_1-genovi.faa
output genovi-temp/contig_1-genovi

Deepnog prediction started

deepnog infer genovi-temp/contig_1-genovi.faa --out genovi-temp/contig_1-genovi_prediction_deepnog.csv -db cog2020 -t 1
[2023-10-08 19:08:43] deepnog.client.client - INFO - Starting deepnog
[2023-10-08 19:08:44] deepnog.client.client - INFO - Loading NN-parameters from /home/siljavah/deepnog_data/cog2020/1/deepnog.pth ...
Traceback (most recent call last):
  File "/home/siljavah/miniconda3/envs/genovi/bin/deepnog", line 8, in <module>
    sys.exit(main())
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/deepnog/client/client.py", line 481, in main
    _start_prediction_or_training(args)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/deepnog/client/client.py", line 295, in _start_prediction_or_training
    return _start_inference(args=args, arch_module=module, arch_cls=cls)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/deepnog/client/client.py", line 324, in _start_inference
    model_dict = torch.load(weights_path, map_location=args.device)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/torch/serialization.py", line 777, in load
    with _open_zipfile_reader(opened_file) as opened_zipfile:
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/torch/serialization.py", line 282, in __init__
    super(_open_zipfile_reader, self).__init__(torch._C.PyTorchFileReader(name_or_buffer))
RuntimeError: PytorchStreamReader failed reading zip archive: failed finding central directory

Deepnog prediction finished succesfully. Predictions saved as genovi-temp/contig_1-genovi_prediction_deepnog.csv

Traceback (most recent call last):
  File "/home/siljavah/miniconda3/envs/genovi/bin/genovi", line 8, in <module>
    sys.exit(main())
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
    visualiseGenome(*get_args())
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 341, in visualiseGenome
    sizes, cogs_p, cogs_n, lengths, chrms, hist, wanted_cogs = base(file, temp_folder + "/" + output_file_part, output_file + "/" + output_file, True, True, cogs_classified, cogs_classified, False, True, deepnog_confidence_threshold, verbose, wanted_cogs=wanted_cogs)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/create_raw.py", line 482, in base
    cogs_dict = get_categories(gbk_file, tmp, deepnog_confidence)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/create_raw.py", line 445, in get_categories
    cogs_df = pd.read_csv(output_pred, sep=',', usecols=['sequence_id', 'prediction'])
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 482, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 811, in __init__
    self._engine = self._make_engine(self.engine)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine
    return mapping[engine](self.f, **self.options)  # type: ignore[call-arg]
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 51, in __init__
    self._open_handles(src, kwds)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/base_parser.py", line 229, in _open_handles
    errors=kwds.get("encoding_errors", "strict"),
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/common.py", line 707, in get_handle
    newline="",
FileNotFoundError: [Errno 2] No such file or directory: 'genovi-temp/contig_1-genovi_prediction_deepnog.csv'

I can get a PNG file if using -cu, but even then I get this error:

There's been an error finding cairoSVG library, so PNG images might be different from expected. Please prefer using SVG output.
/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
  "Premature end of file in sequence data", BiopythonParserWarning
genovi-temp/contig_1-genovi_bands.kar created succesfully.
genovi-temp/contig_1-genovi_tRNA_pos.txt created succesfully.
genovi-temp/contig_1-genovi_tRNA_neg.txt created succesfully.
genovi-temp/contig_1-genovi_rRNA_pos.txt created succesfully.
genovi-temp/contig_1-genovi_rRNA_neg.txt created succesfully.
genovi-temp/contig_1-genovi_CDS_pos.txt created succesfully.
genovi-temp/contig_1-genovi_CDS_neg.txt created succesfully.
Transforming GenBank record tig00000001 to .fna
Done
Drawing 1...
Traceback (most recent call last):
  File "/home/siljavah/miniconda3/envs/genovi/bin/genovi", line 8, in <module>
    sys.exit(main())
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
    visualiseGenome(*get_args())
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 421, in visualiseGenome
    os.rename(output_file + "-contig_" + str(i) + ".png", output_file + "/" + output_file + "-contig_" + str(i) + ".png")
FileNotFoundError: [Errno 2] No such file or directory: 'genovi-contig_1.png' -> 'genovi/genovi-contig_1.png'

Is there any way I could fix this? Just to note, I am just an undergraduate trying to do my bioinformatics project so if I've just done something very obviously wrong then please bare with me!