search

kblin / ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers
Apache License 2.0
956 stars 174 forks source link

KeyError: 'assembly_accession' #225

Closed biotemon closed 5 months ago

biotemon commented 5 months ago

I am trying to run the following line:

ncbi-genome-download bacteria -l 'all' -g 'Pseudomonas' -m metadata.txt

But I get this error:

Traceback (most recent call last):
  File "/Users/tito_miniconda/opt/miniconda3/bin/ncbi-genome-download", line 8, in <module>
    sys.exit(main())
  File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/site-packages/ncbi_genome_download/__main__.py", line 26, in main
    ret = args_download(args)
  File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/site-packages/ncbi_genome_download/core.py", line 174, in args_download
    return config_download(config)
  File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/site-packages/ncbi_genome_download/core.py", line 193, in config_download
    download_candidates = select_candidates(config)
  File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/site-packages/ncbi_genome_download/core.py", line 290, in select_candidates
    for entry in filter_entries(entries, config):
  File "/Users/tito_miniconda/opt/miniconda3/lib/python3.8/site-packages/ncbi_genome_download/core.py", line 336, in filter_entries
    if not config.is_compatible_assembly_accession(entry['assembly_accession']):
KeyError: 'assembly_accession'

What can I do?

kblin commented 5 months ago

Hi there. This sounds like this might be caused by the layout change in the assembly accession file from NCBI almost a year ago. I've released ncbi-genome-download 0.3.2 to address this 11 months ago, please make sure you're on at least that version.

Please leave a comment if you are on a recent version and the problem still exists.