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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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07_taxonomic_discovery_with_sourmash #43

Closed ccbaumler closed 2 years ago

ccbaumler commented 2 years ago

In 07_taxonomic_discovery_with_sourmash at the lca gather step and I receive this error:

(dib_rotation) baumlerc@bm12:~/2020_rotation_project/sourmash$ ls genbank-k31.lca.json SRR1976948_2.fastq.gz SRR1976948_1.fastq.gz SRR1976948.sig

(dib_rotation) baumlerc@bm12:~/2020_rotation_project/sourmash$ 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')

The work around suggested by Dr Titus Brown:

you’ll get decent results from sourmash gather but it won’t be the same. (that is, just omit the lca)