mberacochea
commented
4 years ago Thank you letting us know about the problem. There is a new version of the toolkit (0.7.0), this version won't stop if there is a missing file.
I can confirm that some of the files on that analysis are missing, even though they are listed by the API. I'll look into this and get back to you.
I'm having the following problem when requesting download of certain accession ids for bulk download:
0%| | 0/9 [00:00<?, ?it/sERROR: HTTP Error 404: Not Found | 0/9 [00:00<?, ?it/s] 0%| | 0/9 [00:00<?, ?it/s] 0%| | 0/9 [00:00<?, ?it/s] Traceback (most recent call last): File "/nfs/sw/ebi-metagenomics/ebi-metagenomics-0.6.5/python/bin/mg-toolkit", line 8, in
sys.exit(main())
File "/nfs/sw/ebi-metagenomics/ebi-metagenomics-0.6.5/python/lib/python3.8/site-packages/mg_toolkit/init.py", line 198, in main
return getattr(mg_toolkit, args.tool)(args)
File "/nfs/sw/ebi-metagenomics/ebi-metagenomics-0.6.5/python/lib/python3.8/site-packages/mg_toolkit/bulk_download.py", line 44, in bulk_download
program.run()
File "/nfs/sw/ebi-metagenomics/ebi-metagenomics-0.6.5/python/lib/python3.8/site-packages/mg_toolkit/bulk_download.py", line 213, in run
num_results_processed = self._process_page(res, progress_bar)
File "/nfs/sw/ebi-metagenomics/ebi-metagenomics-0.6.5/python/lib/python3.8/site-packages/mg_toolkit/bulk_download.py", line 253, in _process_page
self.download_file(
File "/nfs/sw/ebi-metagenomics/ebi-metagenomics-0.6.5/python/lib/python3.8/site-packages/mg_toolkit/bulk_download.py", line 163, in download_file
BulkDownloader.download_resource_by_url(
File "/nfs/sw/ebi-metagenomics/ebi-metagenomics-0.6.5/python/lib/python3.8/site-packages/mg_toolkit/bulk_download.py", line 125, in download_resource_by_url
urlretrieve(url, output_file_name)
File "/nfs/sw/python/python-3.8.3/lib/python3.8/urllib/request.py", line 247, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
File "/nfs/sw/python/python-3.8.3/lib/python3.8/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/nfs/sw/python/python-3.8.3/lib/python3.8/urllib/request.py", line 531, in open
response = meth(req, response)
File "/nfs/sw/python/python-3.8.3/lib/python3.8/urllib/request.py", line 640, in http_response
response = self.parent.error(
File "/nfs/sw/python/python-3.8.3/lib/python3.8/urllib/request.py", line 569, in error
return self._call_chain(args)
File "/nfs/sw/python/python-3.8.3/lib/python3.8/urllib/request.py", line 502, in _call_chain
result = func(args)
File "/nfs/sw/python/python-3.8.3/lib/python3.8/urllib/request.py", line 649, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: Not Found