database --default parameters

[Rundon-svg]

Hi Qiyun,

In database.doc,
--default
is equivalent to
--cats microbe --sample 1 --rank species_latin --above --reference --represent --typemater --compile diamond

While the "--manual" used to compare the two command:

1. --default

...
Done.
  Total number of genomes in categories: 263640.
Filtering genomes...
Done.
Filtering genomes by taxonomy...
  Dropped 43 genomes without capitalized organism name.
  Dropped 8 genomes without valid taxId.
Done.
Sampling genomes based on taxonomy...
Up to 1 genome(s) will be sampled per species.
  Sampled 39046 genomes from 39046 species.
Included 16 reference genomes.
Included 17182 representative genomes.
Total number of sampled genomes: 39048.

2. equivalent command

...
Done.
  Total number of genomes in categories: 263640.
Filtering genomes...
Done.
Filtering genomes by taxonomy...
  Dropped 43 genomes without capitalized organism name.
  Dropped 8 genomes without valid taxId.
Done.
Sampling genomes based on taxonomy...
Up to 1 genome(s) will be sampled per species **(Latinate names only)** .
  Sampled 16980 genomes from 16980 species.
Sampling will also be performed on: genus, family, order, class, phylum.
  Sampled 270 more genomes from 270 genera.
  Sampled 0 more genomes from 0 families.
  Sampled 0 more genomes from 0 orders.
  Sampled 0 more genomes from 0 classes.
  Sampled 0 more genomes from 0 phyla.
  Sampled a total of 17250 genomes at species and above.
Included 16 reference genomes.
Included 17182 representative genomes.
Included 19724 type material genomes.
Total number of sampled genomes:   24042.

May the equivalent command add sampled steps? Or something I did wrong in installation and command line?

best,