search

linsalrob / PhiSpy

Prediction of prophages from bacterial genomes
MIT License
70 stars 20 forks source link

ValueError: LOCUS line does not contain - at position 75 in date #70

Open tjcu408 opened 2 months ago

tjcu408 commented 2 months ago

There is an issue when I run PhiSpy on *.gbk files obtained by Prokka, I don't know why.

$ PhiSpy.py -o outfile *.gbk error message: Traceback (most recent call last): File "/home/meta/miniconda3/envs/bacteria/lib/python3.9/site-packages/Bio/File.py", line 72, in as_handle with open(handleish, mode, **kwargs) as fp: TypeError: expected str, bytes or os.PathLike object, not TextIOWrapper

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/meta/miniconda3/envs/bacteria/bin/PhiSpy.py", line 10, in sys.exit(run()) File "/home/meta/miniconda3/envs/bacteria/lib/python3.9/site-packages/PhiSpyModules/main.py", line 122, in run main(sys.argv) File "/home/meta/miniconda3/envs/bacteria/lib/python3.9/site-packages/PhiSpyModules/main.py", line 44, in main args_parser.record = PhiSpyModules.SeqioFilter(filter(lambda x: len(x.seq) > args_parser.min_contig_size, SeqIO.parse(handle, "genbank"))) File "/home/meta/miniconda3/envs/bacteria/lib/python3.9/site-packages/PhiSpyModules/seqio_filter.py", line 33, in init for n, item in enumerate(content): File "/home/meta/miniconda3/envs/bacteria/lib/python3.9/site-packages/Bio/SeqIO/Interfaces.py", line 72, in next return next(self.records) File "/home/meta/miniconda3/envs/bacteria/lib/python3.9/site-packages/Bio/GenBank/Scanner.py", line 516, in parse_records record = self.parse(handle, do_features) File "/home/meta/miniconda3/envs/bacteria/lib/python3.9/site-packages/Bio/GenBank/Scanner.py", line 499, in parse if self.feed(handle, consumer, do_features): File "/home/meta/miniconda3/envs/bacteria/lib/python3.9/site-packages/Bio/GenBank/Scanner.py", line 465, in feed self._feed_first_line(consumer, self.line) File "/home/meta/miniconda3/envs/bacteria/lib/python3.9/site-packages/Bio/GenBank/Scanner.py", line 1443, in _feed_first_line raise ValueError( ValueError: LOCUS line does not contain - at position 75 in date: LOCUS 1 398700 bp DNA linear 25-6月-2024