I have been receiving a message while running the 'prime' step of setting up a configuration file. I am curious if this is causing issues with my analysis. I have been attempting to get treePL to run for awhile now but the CV step takes a long time (over 25 days on a computer cluster) and the priming step always worries me (See below). The tree contains 12,780 tips and was built from a supermatrix. I used ExaML to build the tree. Happy to supply input tree if needed. Thanks for any suggestions on how to proceed.
-----Config file-----
treefile = monocots_rerooted.tre
smooth = .000001
numsites = 7489
mrca = ALISMA Ranalisma_rostratum Echinodorus_bracteatus
min = ALISMA 20
max = ALISMA 20
mrca = APONO Aponogeton_fenestralis Aponogeton_lakhonensis
min = APONO 81.13
max = APONO 81.13
mrca = LEMNOI Lemna_gibba Spirodela_intermedia
min = LEMNOI 66
max = LEMNOI 66
mrca = LOMAN Cordyline_australis Cordyline_pumilio
min = LOMAN 22
max = LOMAN 22
mrca = AGAVO Anemarrhena_asphodeloides Chlorophytum_subpetiolatum
min = AGAVO 14.5
max = AGAVO 16.2
mrca = ASTEL Astelia_alpina Astelia_grandis
min = ASTEL 23.2
max = ASTEL 23.2
mrca = GOODY Pachyplectron_arifolium Gonatostylis_vieillardii
min = GOODY 15
max = GOODY 20
mrca = XANTH Eremurus_stenophyllus Caesia_contorta
min = XANTH 38.0
max = XANTH 47.8
mrca = CYCLAN Carludovica_rotundifolia Cyclanthus_bipartitus
min = CYCLAN 47
max = CYCLAN 47
mrca = RIPO Ripogonum_scandens Ripogonum_elseyanum
min = RIPO 51
max = RIPO 52
mrca = ZINGI Siphonochilus_aethiopicus Rhynchanthus_beesianus
min = ZINGI 72.1
max = ZINGI 83.6
mrca = TYPHA Typha_angustifolia Sparganium_eurycarpum
min = TYPHA 51.66
max = TYPHA 51.66
mrca = CYPER Cladium_mariscus Chorizandra_cymbaria
min = CYPER 47
max = CYPER 47
mrca = DIOSCO Dioscorea_antaly Dioscorea_arachidna
min = DIOSCO 27.23
max = DIOSCO 27.23
mrca = ARECA Phoenix_canariensis Salacca_ramosiana
min = ARECA 83.6
max = ARECA 86.3
outfile = monocot_fixed_dated_sm1e6.tre
prime
randomcv
cv
plsimaniter = 500000
cvsimaniter = 200000
logpen
iterate until convergence, takes longer but a good idea
thorough
number of threads
nthreads = 8
opt =
optad =
optcvad =
--------Example PRIME OUTPUT------
a bunch of 'tiny branch length at internal node. setting to 0.00013352918" warnings
......
preorder prep
calculating character durations
setting min and max
setting up all constraints
getting feasible start dates
start rate 0.00097994697
numparams:12771
initial calc: 5293281.4
LF SIM
exit siman: 764076.6
now priming regular
nfeval: 29 rc: Linear search failed
final: 764076.6 diff: 1.1641532e-10
setting NLOPT: LD_LBFGS
result: -1
final: 763870.27 diff: 206.32594
setting NLOPT: LD_TNEWTON_PRECOND_RESTART
result: 5
final: 729583.62 diff: 34492.973
setting NLOPT: LD_MMA
result: 3
final: 764071.95 diff: 4.6418695
setting NLOPT: LD_VAR2
result: 5
final: 615831.62 diff: 148244.98
setting NLOPT : NLOPT_LD_MMA
you may want to set the plsimaniter > 100000
result: 3
final: 764071.95 diff: 4.6418695
now priming AD
nfeval: 149 rc: Linear search failed
final: 762341.01 diff: 1735.5861
setting NLOPT: LD_LBFGS
result: -1
final: 763870.27 diff: 206.326
setting NLOPT: LD_TNEWTON_PRECOND_RESTART
result: 5
final: 725095.58 diff: 38981.019
setting NLOPT: LD_MMA
result: 3
final: 764071.95 diff: 4.6416944
setting NLOPT: LD_VAR2
result: 5
final: 614199.28 diff: 149877.32
setting NLOPT : NLOPT_LD_MMA
you may want to set the plsimaniter > 100000
result: 3
final: 764071.95 diff: 4.6416944
now priming CV (AD)
nfeval: 330 rc: Linear search failed
final: 640800.97 diff: 123275.63
setting NLOPT parallel : LD_LBFGS
result: -1
final: 763629.47 diff: 447.12907
setting NLOPT parallel : LD_TNEWTON_PRECOND_RESTART
result: 5
final: 756486.44 diff: 7590.1535
setting NLOPT parallel : LD_MMA
result: 4
final: 648082.5 diff: 115994.1
setting NLOPT parallel : LD_VAR2
result: 5
final: 625347.82 diff: 138728.78
setting NLOPT parallel : LD_MMA
you may want to set the plsimaniter > 100000
result: 4
final: 648082.5 diff: 115994.1
best: 4(0) bestad: 4 (0) bestcv: 4 (0)
PLACE THE LINES BELOW IN THE CONFIGURATION FILE
opt = 4
optad = 4
optcvad = 4
------END-----
Hello everyone,
I have been receiving a message while running the 'prime' step of setting up a configuration file. I am curious if this is causing issues with my analysis. I have been attempting to get treePL to run for awhile now but the CV step takes a long time (over 25 days on a computer cluster) and the priming step always worries me (See below). The tree contains 12,780 tips and was built from a supermatrix. I used ExaML to build the tree. Happy to supply input tree if needed. Thanks for any suggestions on how to proceed.
-----Config file----- treefile = monocots_rerooted.tre smooth = .000001 numsites = 7489 mrca = ALISMA Ranalisma_rostratum Echinodorus_bracteatus min = ALISMA 20 max = ALISMA 20 mrca = APONO Aponogeton_fenestralis Aponogeton_lakhonensis min = APONO 81.13 max = APONO 81.13 mrca = LEMNOI Lemna_gibba Spirodela_intermedia min = LEMNOI 66 max = LEMNOI 66 mrca = LOMAN Cordyline_australis Cordyline_pumilio min = LOMAN 22 max = LOMAN 22 mrca = AGAVO Anemarrhena_asphodeloides Chlorophytum_subpetiolatum min = AGAVO 14.5 max = AGAVO 16.2 mrca = ASTEL Astelia_alpina Astelia_grandis min = ASTEL 23.2 max = ASTEL 23.2 mrca = GOODY Pachyplectron_arifolium Gonatostylis_vieillardii min = GOODY 15 max = GOODY 20 mrca = XANTH Eremurus_stenophyllus Caesia_contorta min = XANTH 38.0 max = XANTH 47.8 mrca = CYCLAN Carludovica_rotundifolia Cyclanthus_bipartitus min = CYCLAN 47 max = CYCLAN 47 mrca = RIPO Ripogonum_scandens Ripogonum_elseyanum min = RIPO 51 max = RIPO 52 mrca = ZINGI Siphonochilus_aethiopicus Rhynchanthus_beesianus min = ZINGI 72.1 max = ZINGI 83.6 mrca = TYPHA Typha_angustifolia Sparganium_eurycarpum min = TYPHA 51.66 max = TYPHA 51.66 mrca = CYPER Cladium_mariscus Chorizandra_cymbaria min = CYPER 47 max = CYPER 47 mrca = DIOSCO Dioscorea_antaly Dioscorea_arachidna min = DIOSCO 27.23 max = DIOSCO 27.23 mrca = ARECA Phoenix_canariensis Salacca_ramosiana min = ARECA 83.6 max = ARECA 86.3 outfile = monocot_fixed_dated_sm1e6.tre prime
randomcv
cv
plsimaniter = 500000 cvsimaniter = 200000 logpen
iterate until convergence, takes longer but a good idea
thorough
number of threads
nthreads = 8
opt =
optad =
optcvad =
--------Example PRIME OUTPUT------ a bunch of 'tiny branch length at internal node. setting to 0.00013352918" warnings ...... preorder prep calculating character durations setting min and max setting up all constraints getting feasible start dates start rate 0.00097994697 numparams:12771 initial calc: 5293281.4 LF SIM exit siman: 764076.6 now priming regular nfeval: 29 rc: Linear search failed final: 764076.6 diff: 1.1641532e-10 setting NLOPT: LD_LBFGS result: -1 final: 763870.27 diff: 206.32594 setting NLOPT: LD_TNEWTON_PRECOND_RESTART result: 5 final: 729583.62 diff: 34492.973 setting NLOPT: LD_MMA result: 3 final: 764071.95 diff: 4.6418695 setting NLOPT: LD_VAR2 result: 5 final: 615831.62 diff: 148244.98 setting NLOPT : NLOPT_LD_MMA you may want to set the plsimaniter > 100000 result: 3 final: 764071.95 diff: 4.6418695
now priming AD nfeval: 149 rc: Linear search failed final: 762341.01 diff: 1735.5861 setting NLOPT: LD_LBFGS result: -1 final: 763870.27 diff: 206.326 setting NLOPT: LD_TNEWTON_PRECOND_RESTART result: 5 final: 725095.58 diff: 38981.019 setting NLOPT: LD_MMA result: 3 final: 764071.95 diff: 4.6416944 setting NLOPT: LD_VAR2 result: 5 final: 614199.28 diff: 149877.32 setting NLOPT : NLOPT_LD_MMA you may want to set the plsimaniter > 100000 result: 3 final: 764071.95 diff: 4.6416944
now priming CV (AD) nfeval: 330 rc: Linear search failed final: 640800.97 diff: 123275.63 setting NLOPT parallel : LD_LBFGS result: -1 final: 763629.47 diff: 447.12907 setting NLOPT parallel : LD_TNEWTON_PRECOND_RESTART result: 5 final: 756486.44 diff: 7590.1535 setting NLOPT parallel : LD_MMA result: 4 final: 648082.5 diff: 115994.1 setting NLOPT parallel : LD_VAR2 result: 5 final: 625347.82 diff: 138728.78 setting NLOPT parallel : LD_MMA you may want to set the plsimaniter > 100000 result: 4 final: 648082.5 diff: 115994.1 best: 4(0) bestad: 4 (0) bestcv: 4 (0) PLACE THE LINES BELOW IN THE CONFIGURATION FILE opt = 4 optad = 4 optcvad = 4 ------END-----