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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!
The text was updated successfully, but these errors were encountered:
Hello!
I keep getting this error when trying to run my genome:
I can get a PNG file if using -cu, but even then I get this error:
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!
The text was updated successfully, but these errors were encountered: