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wtmatlock / flanker

Gene-flank analysis tool
MIT License
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Dependency problems since Conda update #50

Closed nenadmacesic closed 2 years ago

nenadmacesic commented 2 years ago

Hi,

I've previously used Flanker without issues but recently had to re-install it. Since then I have kept having the same error message despite running the same commands that worked successfully previously. Any tips much appreciated:

Traceback (most recent call last): File "/home/ubuntu/miniconda3/envs/flanker/bin/flanker", line 8, in sys.exit(main()) File "/home/ubuntu/miniconda3/envs/flanker/lib/python3.7/site-packages/flanker/flanker.py", line 618, in main flanker_main() File "/home/ubuntu/miniconda3/envs/flanker/lib/python3.7/site-packages/flanker/flanker.py", line 570, in flanker_main args.fasta_file, args.window, gene.strip()) File "/home/ubuntu/miniconda3/envs/flanker/lib/python3.7/site-packages/flanker/flanker.py", line 421, in flank_fasta_file_lin data = pd.read_csv(unfiltered_abricate_file, sep='\t', header=0) File "/home/ubuntu/miniconda3/envs/flanker/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, kwargs) File "/home/ubuntu/miniconda3/envs/flanker/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/home/ubuntu/miniconda3/envs/flanker/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 482, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/home/ubuntu/miniconda3/envs/flanker/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 811, in init self._engine = self._make_engine(self.engine) File "/home/ubuntu/miniconda3/envs/flanker/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/ubuntu/miniconda3/envs/flanker/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 69, in init self._reader = parsers.TextReader(self.handles.handle, kwds) File "pandas/_libs/parsers.pyx", line 549, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

nenadmacesic commented 2 years ago

Hi - this problem was solved by troubleshooting things in Abricate. It looks like a problem with the version of BLAST used with Abricate. Please see here for full details: https://github.com/tseemann/abricate/issues/164

bede commented 2 years ago

Hi @nenadmacesic, thank you for reporting your experience. Were you able to fix this issue using abricate --setupdb?

Do you think we should be pinning a specific version of Abricate and/or BLAST?