kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
7 stars 1 forks source link

ValueError: unknown url type: '' #87

Closed kfuku52 closed 2 years ago

kfuku52 commented 2 years ago
trying to fetch SRR6008323 from 
Traceback (most recent call last):
  File "/opt/conda/envs/biotools/bin/amalgkit", line 378, in <module>
    args.handler(args)
  File "/opt/conda/envs/biotools/bin/amalgkit", line 33, in command_getfastq
    getfastq_main(args)
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/amalgkit/getfastq.py", line 815, in getfastq_main
    download_sra(metadata, sra_stat, args, output_dir, overwrite=False)
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/amalgkit/getfastq.py", line 234, in download_sra
    urllib.request.urlretrieve(str(sra_source), os.path.join(work_dir, (str(sra_id + '.sra'))))
  File "/opt/conda/envs/biotools/lib/python3.9/urllib/request.py", line 239, in urlretrieve
    with contextlib.closing(urlopen(url, data)) as fp:
  File "/opt/conda/envs/biotools/lib/python3.9/urllib/request.py", line 214, in urlopen
    return opener.open(url, data, timeout)
  File "/opt/conda/envs/biotools/lib/python3.9/urllib/request.py", line 501, in open
    req = Request(fullurl, data)
  File "/opt/conda/envs/biotools/lib/python3.9/urllib/request.py", line 320, in __init__
    self.full_url = url
  File "/opt/conda/envs/biotools/lib/python3.9/urllib/request.py", line 346, in full_url
    self._parse()
  File "/opt/conda/envs/biotools/lib/python3.9/urllib/request.py", line 375, in _parse
    raise ValueError("unknown url type: %r" % self.full_url)
ValueError: unknown url type: ''