ValueError: u'clade' is not in list

[santcamille]

Hello, I'm trying to use taxtable. I first ran: taxit new_database taxonomy.db Then I tried to use taxtable: taxit taxtable taxonomy.db -f tax_ids.txt -o taxa.csv but I get the error:

Traceback (most recent call last):
  File "/home/pc/taxtastic/taxtastic_env_bis/bin/taxit", line 8, in <module>
    sys.exit(main())
  File "/home/pc/taxtastic/taxtastic_env_bis/local/lib/python2.7/site-packages/taxtastic/scripts/taxit.py", line 51, in main
    return action(arguments)
  File "/home/pc/taxtastic/taxtastic_env_bis/local/lib/python2.7/site-packages/taxtastic/subcommands/taxtable.py", line 150, in action
    sorted_ranks = sorted(all_ranks, key=order_ranks(tax.ranks[::-1]))
  File "/home/pc/taxtastic/taxtastic_env_bis/local/lib/python2.7/site-packages/taxtastic/subcommands/taxtable.py", line 77, in _inner
    return (ref_ranks.index(rank), 0)
ValueError: u'clade' is not in list

I also tried: taxit taxtable taxonomy.db -t 1280 And I get the same error message.

I'm using taxtastic v0.8.11

I'm not sure what is going on but I checked and the NCBI taxonomy database had just been updated, maybe that's why... Thanks

[crosenth]

Hi santcamille, I believe this is related to Issue https://github.com/fhcrc/taxtastic/issues/133 which we will have a fix for shortly. Thank you for raising this Issue

[crosenth]

Please see version v0.9.0 - https://github.com/fhcrc/taxtastic/releases/tag/v0.9.0