Number of independent branch combinations: 0

[kfuku52]

In an insect cuticle protein dataset (HOG0000403), no combination was found with:

• --exhaustive_until 1 --fg_exclude_wg yes --fg_stem_only yes
• --exhaustive_until 1 --fg_exclude_wg yes --fg_stem_only no

  Arity = 2: Generating cb table
  Arity = 2: Targeted search of foreground branch combinations
  All branches: 524
  Number of redundant branch combination unions: 190
  Number of target branches: 20
  Number of independent/non-independent branch combinations: 190
  Removing 0 non-independent branch combinations.
  removing 190 (out of 190) dependent foreground branch combinations.
  Time elapsed for generating branch combinations: 1 sec
  Number of independent branch combinations: 0

With --exhaustive_until 1 --fg_exclude_wg no --fg_stem_only yes, I got:

Arity = 2: Generating cb table
Arity = 2: Targeted search of foreground branch combinations
All branches: 524
Number of redundant branch combination unions: 190
Number of target branches: 20
Number of independent/non-independent branch combinations: 190
Removing 0 non-independent branch combinations.
Time elapsed for generating branch combinations: 0 sec
Number of independent branch combinations: 190

With --exhaustive_until 1 --fg_exclude_wg no --fg_stem_only no, I got:

Arity = 2: Generating cb table
Arity = 2: Targeted search of foreground branch combinations
All branches: 524
Number of redundant branch combination unions: 9,730
Number of target branches: 140
Number of independent/non-independent branch combinations: 9,730
Removing 478 non-independent branch combinations.
Time elapsed for generating branch combinations: 1 sec
Number of independent branch combinations: 9,252

--fg_exclude_wg yes is not working correctly in some conditions? This problem didn't appear with the PGK dataset.

[kfuku52]

This turned out to be a correct behavior, not a bug. foreground.txt was specified as below, making all foreground lineages "within a group".

1   Adela_reaumurella_.*
1   Agrilus_planipennis_.*
1   Altica_viridicyanea_.*
1   Aricia_agestis_.*
1   Calliphora_vicina_.*
...