kfuku52/radte

Divergence time estimation in the complex history of gene family evolution

radte's Issues

2 distinct errors

Hello,

Some gene trees seem to give two distinct error messages and I could not figure out why. I used default setting and the same species tree in both cases.
Here it is the first one:

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.

And the other one:

NULL
Error in `[<-.data.frame`(`*tmp*`, ind, "lower_sp_node", value = c("s23",  :
  replacement has 2 rows, data has 1
Calls: [<- -> [<-.data.frame
Execution halted

I have attached 2 gene
trees which produce the two distinct errors, with the species tree.
errorneous_gene_trees.zip

Thank you for your help in advance!

Cheers

Supporting interval estimates as input

Error for gene tree processing

Hi everyone:
I try to run the RADTE program using my dataset. I replaced "_" into "." in gene id, and modified species name into "genus_speicies". Then I executed Notung-2.9.1.5 to produce the rooted gene tree, with "--resolve" model used to avoid the polytomies.
My issue is that there is an error after "calibration node removed" when I ran RADTE, showing that "All attempts for divergence time estimation were failed. Exiting":

I can't figure out the reason for this error，have anyone met this error before?

Error in gene tree processing

Hello,

First of all let me thank you for setting up this tool, been searching for something like it before. I tried to follow the tutorial provided with my own dataset and provided the same parameters as in the the tutorial, but got the following error message:

Start: species tree processing
Read 1 item
Minimum edge length: 0
Number of short edges ( length < 0.001 ): 6
Transfering branch length from edge 22 to 23 and 60
Transfering branch length from edge 28 to 29 and 50
Transfering branch length from edge 33 to 34 and 37
Transfering branch length from edge 39 to 40 and 43
Transfering branch length from edge 51 to 52 and 59
The tree is not ultrametric. Adjusting the branch length.
Total branch length difference between before- and after-adjustment: 0.0004614733
Nonzero tip age(s) were detected (max=1.4210854715202e-14). Coercing to 0.
End: species tree processing

Start: gene tree processing
Reading NOTUNG tree.
[1] "n2" "n5" "n6"
 Named int [1:3] 12 15 16
 - attr(*, "names")= chr [1:3] "n2" "n5" "n6"
NULL
Error in x[[jj]][iseq] <- vjj : replacement has length zero
Calls: [<- -> [<-.data.frame
In addition: Warning message:
In min(sp_node_table$age[sapply(sp_node_table$spp, function(x) { :
  no non-missing arguments to min; returning Inf

What do you think I am doing wrong?

Cheers

Supporting mcmctree-ready outputs

All attempts for divergence time estimation were failed. Exiting.

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.

drop rkftools dependency