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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 #61

Open nkavaler1 opened 1 year ago

nkavaler1 commented 1 year ago

When trying to run

sourmash lca gather -o SRR1976948_lca_gather.csv SRR1976948.sig genbank-k31.lca.json

this is the result:

(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')

sourmash lca no longer used for taxonomic analysis, (use sourmash tax summarize instead?) in the documentations it is no longer a command

ctb commented 10 months ago

Thanks for noticing this!

the updated commands should be something like this:

sourmash gather SRR1976948.sig <gtdb database.zip> -o SRR1976948_gather.csv
sourmash tax metagenome -g SRR1976948_gather.csv -t <gtdb taxonomy>