Error when model isn't specified

[erinyoung]

Thank you for your continued efforts to maintain this software! I've found it very useful.

I'm currently switching to using version 1.5.8.

I get a weird error when I don't specify a model for artic minion:

$ artic minion --normalise 200  --threads 4 --read-file SRR22452250_1_filtered.fastq.gz --bed new.primer.bed --ref reference.fasta finalish
Traceback (most recent call last):
  File "/home/eriny/miniconda3/envs/artic/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/eriny/miniconda3/envs/artic/bin/artic", line 10, in <module>
    sys.exit(main())
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/site-packages/artic/pipeline.py", line 300, in main
    args.func(parser, args)
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/site-packages/artic/pipeline.py", line 28, in run_subtool
    submodule.run(parser, args)
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/site-packages/artic/minion.py", line 61, in run
    model = choose_model(args.read_file)
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/site-packages/artic/utils.py", line 870, in choose_model
    read = next(reads)
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/site-packages/Bio/SeqIO/Interfaces.py", line 91, in __next__
    return next(self.records)
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/site-packages/Bio/SeqIO/QualityIO.py", line 1099, in iterate
    for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/site-packages/Bio/SeqIO/QualityIO.py", line 929, in FastqGeneralIterator
    line = next(handle)
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/gzip.py", line 313, in read1
    return self._buffer.read1(size)
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/_compression.py", line 68, in readinto
    data = self.read(len(byte_view))
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/gzip.py", line 487, in read
    if not self._read_gzip_header():
  File "/home/eriny/miniconda3/envs/artic/lib/python3.9/gzip.py", line 435, in _read_gzip_header
    raise BadGzipFile('Not a gzipped file (%r)' % magic)
gzip.BadGzipFile: Not a gzipped file (b'@S')

Everything works fine when I specify the model.

[BioWilko]

I think the issue is that your fastq file isn't actually gzipped, if you do head SRR22452250_1_filtered.fastq.gz do you see the read data?
If so, try renaming the file to SRR22452250_1_filtered.fastq and it should work fine.

I can look at adding some handling to check that the file is actually compressed but I'm not sure that it would be a good idea to silently handle this since the error is fairly descriptive...

[github-actions]

This issue is stale because it has been open for 30 days with no activity.