Sourmash lca gather not a command anymore

dib-lab / dib_rotation

Metagenomics DIB-lab rotation project

https://dib-lab.github.io/dib_rotation/

BSD 3-Clause "New" or "Revised" License

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Sourmash lca gather not a command anymore #70

Closed nkavaler1 closed 7 months ago

nkavaler1 commented 10 months ago

When attempting to run sourmash lca gather during the "Taxonomic Discovery with Sourmash" section, this error message is sent:

(dib_rotation) nkavaler@bm16:~$ sourmash lca gather -o SRR1976948_lca_gather.csv SRR1976948.sig genbank-k31.lca.json
 lca: error: argument subcmd: invalid choice: 'gather' (choose from 'classify', 'compare', 'compare_csv', 'index', 'rankinfo', 'summarize')

use sourmash tax now instead?

ccbaumler commented 7 months ago

fixed with 5a5adb9 and 5301ff1