This is my first run with treePL program for priming analysis and got message like
set thorough: true (MAY TAKE A WHILE)
setting log penalty
PRIMING the optimization parameters and then exiting
outfile: prime_outTreeRax
finished reading config file
using system clock for random number seed = 1611032383
tiny branch length at internal node. setting to 5.2042675e-06
problem with mrca DIP (probably no mrca named this)
But no output file has been generated even I have multiplied branch length with 10^6 following Kévin J. L. Maurin tutorial, but the this tiny branch length message is coming. Moreover I could not understand why the mrca could not recognizes DIP that I have already mentioned in the config file.
My configuration file is like that
[1 Input tree]
treefile = 335TemTRax10e6.tre
[2 General command]
numsites = 192150
thorough
log_pen
[3 Calibration command]
mrca DIP taxon23 taxon42
min = DIP 230
max = DIP 290
mrca TRE taxon15 taxon43
max = TRE 325
[4 Priming command]
prime
[5 Best optimisation param]
[6 Cross-validation analysis]
[7 Best smooting value]
[8 Output]
outfile = prime_outTreeRax
Dear Experts,
This is my first run with treePL program for priming analysis and got message like
But no output file has been generated even I have multiplied branch length with 10^6 following Kévin J. L. Maurin tutorial, but the this tiny branch length message is coming. Moreover I could not understand why the mrca could not recognizes DIP that I have already mentioned in the config file. My configuration file is like that
And Tree File is
((((((taxon49:10000000,((((taxon42:2000000,(taxon45:1000000,taxon46:1000000):1000000):1000000,taxon52:3000000):2000000,(taxon37:4000000,((taxon38:1000000,taxon41:1000000):2000000,((taxon40:1000000,taxon39:1000000):1000000,taxon36:2000000):1000000):1000000):1000000):4000000,((taxon20:4000000,(taxon54:3000000,(taxon17:2000000,(taxon18:1000000,taxon16:1000000):1000000):1000000):1000000):4000000,(taxon35:7000000,(taxon50:6000000,((taxon29:4000000,((taxon51:2000000,(taxon32:1000000,taxon26:1000000):1000000):1000000,(taxon53:1000000,taxon33:1000000):2000000):1000000):1000000,((taxon34:1000000,taxon27:1000000):2000000,((taxon31:1000000,taxon28:1000000):1000000,taxon30:2000000):1000000):2000000):1000000):1000000):1000000):1000000):1000000):1000000,taxon25:11000000):1000000,(((taxon24:1000000,taxon19:1000000):2000000,((taxon21:1000000,taxon22:1000000):1000000,(taxon48:1000000,taxon47:1000000):1000000):1000000):8000000,(taxon44:10000000,(taxon1:9000000,(((taxon14:1000000,taxon4:1000000):6000000,((taxon7:1000000,taxon9:1000000):5000000,((taxon8:4000000,(((taxon11:1000000,taxon3:1000000):1000000,taxon13:2000000):1000000,taxon5:3000000):1000000):1000000,((taxon6:1000000,taxon12:1000000):1000000,taxon10:2000000):3000000):1000000):1000000):1000000,taxon2:8000000):1000000):1000000):1000000):1000000):1000000,taxon23:13000000):1000000,taxon43:14000000):7500000,taxon15:7500000);
It will be an immense help if someone kindly correct me.