starts, then fail

Hi,

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!

[kblin]

Thanks for the great analysis (and the patch in #87). I’ll reopen the issue until the fix is in a release.

[kblin]

Reopening issues where fix hasn’t been shipped yet.