starts, then fail
See original GitHub issueHi,
I try to download all viral reference genomes in refseq like so:
ncbi-genome-download --format fasta --section refseq --verbose --parallel 10 --human-readable viral
The program starts downloading things but then, at the same ID (GCF…) breaks with the following error message:
INFO: Downloading record 'GCF_000868825.1'
INFO: Downloading record 'GCF_000844105.1'
Traceback (most recent call last):
File "/Users/pi/.virtualenvs/lab3/bin/ncbi-genome-download", line 11, in <module>
sys.exit(main())
File "/Users/pi/.virtualenvs/lab3/lib/python3.5/site-packages/ncbi_genome_download/__main__.py", line 73, in main
ret = ncbi_genome_download.download(args)
File "/Users/pi/.virtualenvs/lab3/lib/python3.5/site-packages/ncbi_genome_download/core.py", line 60, in download
args.taxid, args.human_readable, args.parallel)
File "/Users/pi/.virtualenvs/lab3/lib/python3.5/site-packages/ncbi_genome_download/core.py", line 75, in _download
for entry in entries:
File "/Users/pi/.virtualenvs/lab3/lib/python3.5/site-packages/ncbi_genome_download/summary.py", line 28, in __next__
entry[self._fields[i]] = val
IndexError: list index out of range
I tried a minimal version as well, same result:
ncbi-genome-download --verbose --parallel 10 viral
Am I using it wrongly or is this an uncaught error, like some empty entry in the database or similar.
Thanks a lot!
Issue Analytics
- State:
- Created 7 years ago
- Comments:26 (17 by maintainers)
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Thanks for the great analysis (and the patch in #87). I’ll reopen the issue until the fix is in a release.
Reopening issues where fix hasn’t been shipped yet.