Closed ccbaumler closed 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')
(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)
sourmash gather
lca
In 07_taxonomic_discovery_with_sourmash at the lca gather step and I receive this error:
The work around suggested by Dr Titus Brown: