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kfuku52 / RADTE

Divergence time estimation in the complex history of gene family evolution
MIT License
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All attempts for divergence time estimation were failed. Exiting. #6

Closed kfuku52 closed 1 year ago

kfuku52 commented 1 year ago 
RADTE version: 0.2.0 
ape version: 5.6.2 
rkftools version: 0.0.1 
R version 4.1.2 (2021-11-01) 
RADTE run_mode: batch 
arguments:
species_tree = /gfe_data/species_tree/dated_species_tree.generax.nwk 
generax_nhx = /gfe_data/orthogroup/generax.tree/OG0006851.generax.nhx 
max_age = 1000 
chronos_lambda = 1 
chronos_model = discrete 
pad_short_edge = 0.001 

--generax_nhx was detected. GeneRax mode. 

Start: species tree processing 
Read 1 item
Minimum edge length: 5.6516 
Number of short edges ( length < 0.001 ): 0 
The tree is not ultrametric. Adjusting the branch length.
Total branch length difference between before- and after-adjustment: 0.001273899 
Nonzero tip age(s) were detected (max=2.8421709430404e-14). Coercing to 0.
End: species tree processing 

Start: gene tree processing 
Reading GeneRax tree.
1 out of 54 branches have small length. Padding with 0.001.
Minimum branch length in gene tree: 0.001 
End: gene tree processing 

# species in the gene tree: 19 
Species in the gene tree: Oryza_sativa, Aldrovanda_vesiculosa, Dionaea_muscipula, Drosera_spatulata, Drosophyllum_lusitanicum, Ancistrocladus_abbreviatus, Nepenthes_gracilis, Triphyophyllum_peltatum, Hylocereus_undatus, Spinacia_oleracea, Beta_vulgaris, Amaranthus_hypochondriacus, Vitis_vinifera, Arabidopsis_thaliana, Populus_trichocarpa, Cephalotus_follicularis, Averrhoa_carambola, Aquilegia_coerulea, Amborella_trichopoda 
Divergence time of the parent species tree clade: 1000 
Divergence time of the MRCA species tree clade: 193.0061 
calibration node removed because of the constraint identical to or greater than one of the upper nodes (name/id/lower/upper):
n28/31/1000/193.0061 
n79/34/1000/193.0061 
n55/36/1000/193.0061 
n31/40/1000/193.0061 
n76/48/1000/193.0061 
n70/50/1000/193.0061 
n82/52/1000/193.0061 
n91/53/1000/193.0061 

Number of constrained speciation nodes: 19 
Number of constrained duplication nodes: 0 

chronos, calibrated nodes: RS 

Setting initial dates...
Fitting in progress... get a first set of estimates
Error in if (sum(freq) > 1) return(-1e+100) : 
  missing value where TRUE/FALSE needed

chronos, calibrated nodes: S 

Setting initial dates...
Fitting in progress... get a first set of estimates
         (Penalised) log-lik = -34.34865 
Optimising rates... frequencies...Error in if (sum(freq) > 1) return(-1e+100) : 
  missing value where TRUE/FALSE needed

chronos, calibrated nodes: R 

Setting initial dates...
Fitting in progress... get a first set of estimates
Error in if (sum(freq) > 1) return(-1e+100) : 
  missing value where TRUE/FALSE needed
All attempts for divergence time estimation were failed. Exiting.
kfuku52 commented 1 year ago

This error was obtained on Linux, but it didn't reproduce on Intel Mac.

RADTE version: 0.2.0 
ape version: 5.6.2 
rkftools version: 0.0.1 
R version 4.1.1 (2021-08-10) 

...

chronos, calibrated nodes: RS 

Setting initial dates...
Fitting in progress... get a first set of estimates
         (Penalised) log-lik = -33.32539 
Optimising rates... frequencies... dates... -33.32539 
Optimising rates... frequencies... dates... -32.49264 
Optimising rates... frequencies... dates... -32.49223 

log-Lik = -32.49222 
PHIIC = 118.98