blackrim / treePL

Phylogenetic penalized likelihood
https://github.com/blackrim/treePL/wiki
GNU General Public License v3.0
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Problem with mrca and tiny branch length at internal node. #55

Closed BiodeB closed 3 years ago

BiodeB commented 3 years ago

Dear Experts,

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

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.

BiodeB commented 3 years ago

Apology, This is a silly mistake = needed after mrcain the config file. However the tiny branch length message is still persist.