failures to converge, what to do in general?

[blackrim]

failures to converge, what to do in general?

[blackrim]

Happy to help.
Seems like the problem here is simply that NFos4 and NFos5 point to the
same node. So treePL doesn't know what to do. I can put in a little catch
and error message for that which would help both of us I think.

On Fri, May 29, 2015 at 9:10 AM, Rutger Vos [email protected]
wrote:

Hi Stephen,

we are intermittently running into the issue that treePL fails to arrive
at feasible starting rates/dates after 10 attempts. This appears to happen
with some combinations of calibration points, but it is not obvious to
either @hettling https://github.com/hettling or me what these
combinations are and what we might be able to do about it in the general
case. Here is a typical example. This is our command file:

treefile = /tmp/XULshU8_lq
smooth = 100
numsites = 26164
outfile = /tmp/VU_SAflRaW
nthreads = 8
seed = 1234
mrca = NFos3 9593 9597 9598 9606
max = NFos3 6.3
min = NFos3 6.3
mrca = NFos4 9593 9597 9598 9600 9606
max = NFos4 15.2
min = NFos4 15.2
mrca = NFos9 100224 164648 170207 222416 33548 36226 36231 373033 43780 54131 54133 54135 54180 61621 61622 75567 78451 78452 88029 9530 9532 9534 9538 9544 9546 9557 9561 9565 9568
max = NFos9 16.8
min = NFos9 16.8
mrca = NFos5 29089 61851 61852 9580 9588 9590 9593 9597 9598 9600 9606
max = NFos5 18.8
min = NFos5 18.8
mrca = NFos1 100224 164648 170207 222416 29089 33548 36226 36231 373033 43780 54131 54133 54135 54180 61621 61622 61851 61852 75567 78451 78452 88029 9530 9532 9534 9538 9544 9546 9557 9561 9565 9568 9580 9588 9590 9593 9597 9598 9600 9606
max = NFos1 32.8
min = NFos1 32.8
mrca = NFos6 100224 118643 164648 170207 198627 222416 29089 30588 30589 30594 30596 30598 33548 36226 36231 373033 43777 43780 52231 54131 54133 54135 54180 57375 58710 61621 61622 61851 61852 66265 70814 70825 70928 75567 78451 78452 867331 88029 9487 9491 9495 9502 9505 9508 9514 9515 9519 9523 9525 9530 9532 9534 9538 9544 9546 9557 9561 9565 9568 9580 9588 9590 9593 9597 9598 9600 9606
max = NFos6 49.8
min = NFos6 49.8
mrca = NFos8 101278 111174 122222 122232 122246 122248 13514 13557 261734 261736 261739 30601 30608 30609 30611 31869 34829 34830 47177 47180 78583 78866 83281 89672 9447 9455 9460 9463 9468 9470 9472
max = NFos8 51.6
min = NFos8 51.6
mrca = NFos7 100224 101278 111174 118643 122222 122232 122246 122248 13514 13557 164648 170207 198627 222416 261734 261736 261739 29089 30588 30589 30594 30596 30598 30601 30608 30609 30611 31869 33548 34829 34830 36226 36231 373033 43777 43780 47177 47180 52231 54131 54133 54135 54180 57375 58710 61621 61622 61851 61852 662464 66265 70814 70825 70928 75567 78451 78452 78583 78866 83281 867331 88029 89672 9447 9455 9460 9463 9468 9470 9472 9478 9487 9491 9495 9502 9505 9508 9514 9515 9519 9523 9525 9530 9532 9534 9538 9544 9546 9557 9561 9565 9568 9580 9588 9590 9593 9597 9598 9600 9606
max = NFos7 77.5
min = NFos7 77.5

This is our tree:

(((((9472:0.011024,261739:0.013202):0.013202,((9463:0.013202,30611:0.021228):0.007521,((89672:0.013202,111174:0.013202):0.013202,(261736:0.007074,30609:0.013202):0.013202):0.013202):0.013202):0.013202,((9470:0.013202,101278:0.013202):0.013202,9468:0.028992):0.010664):0.013202,(((((9460:0.009639,47177:0.013202):0.001311,(((30608:0.013202,122232:0.013202):0.013202,47180:0.013202):0.012450,122248:0.013202):0.013202):0.024734,(((13514:0.008638,34829:0.013202):0.000200,9455:0.013202):0.014976,(9447:0.002842,(13557:0.013202,122222:0.018402):0.013202):0.012615):0.007645):0.004486,(((78866:0.046375,78583:0.013202):0.013202,261734:0.013202):0.007734,(122246:0.047206,(30601:0.010266,83281:0.006046):0.013202):0.013202):0.013202):0.001244,(34830:0.029978,31869:0.013202):0.013202):0.007373):0.013202,((662464:0.013202,9478:0.013202):0.013202,(((((9523:0.013202,9525:0.013202):0.001399,70814:0.021428):0.004367,((30598:0.005837,43777:0.008787):0.013202,(30596:0.013202,70825:0.000622):0.011
371):0.013202):0.013202,(((((30588:0.000090,58710:0.013202):0.013202,(9495:0.013202,(57375:0.001958,52231:0.013202):0.011134):0.001295):0.013202,(9487:0.013202,9491:0.003918):0.013202):0.013202,((9515:0.013202,9514:0.013202):0.012203,(66265:0.011246,70928:0.013202):0.002650):0.000480):0.000208,(((9502:0.013202,30589:0.004507):0.003904,((118643:0.002554,9508:0.000929):0.011049,(9519:0.006771,30594:0.013202):0.000442):0.013202):0.013202,(9505:0.013202,867331:0.002739):0.013202):0.013202):0.004358):0.013202,(((((9597:0.000097,9598:0.002133):0.013202,9593:0.013202):0.001745,((((61851:0.013202,36231:0.013202):0.013202,(9588:0.013202,9580:0.000872):0.004219):0.013202,((29089:0.013202,61852:0.013202):0.013202,9590:0.013202):0.000448):0.003998,9600:0.008932):0.000766):0.007699,9606:0.013202):0.004165,((((75567:0.013202,(9544:0.013202,9546:0.001363):0.001126):0.013202,((9557:0.013202,9565:0.013202):0.013202,(9568:0.001191,((9530:0.003512,9532:0.013202):0.013202,9561:0.013202):0.001271):0.013
202):0.000289):0.003910,(((100224:0.006358,9534:0.013202):0.013202,(198627:0.000171,36226:0.002060):0.013202):0.013202,(9538:0.000140,54135:0.013202):0.013202):0.000888):0.001384,((((43780:0.013202,170207:0.013202):0.001246,((54133:0.002705,(78452:0.013202,78451:0.001786):0.013202):0.013202,(61621:0.007952,61622:0.002124):0.002263):0.004169):0.000402,(54180:0.013202,(222416:0.001048,88029:0.001168):0.001743):0.000565):0.013202,(164648:0.013202,(373033:0.005325,(33548:0.026403,54131:0.000348)r1:0.000000):0.000000):0.026403):0.013202):0.013202):0.013202):0.013202):0.004509);

And this is the treePL log:

outfile: /tmp/VU_SAflRaW
setting the maximum number of threads to 8
setting the random number seed to 1234
finished reading config file
tiny branch length at internal node. setting to 3.8220456e-05
tiny branch length at internal node. setting to 3.8220456e-05
tiny branch length at internal node. setting to 3.8220456e-05
setting NFos1 min: 32.8
setting NFos3 min: 6.3
setting NFos4 min: 15.2
setting NFos5 min: 18.8
setting NFos6 min: 49.8
setting NFos7 min: 77.5
setting NFos8 min: 51.6
setting NFos9 min: 16.8
setting NFos1 max: 32.8
setting NFos3 max: 6.3
setting NFos4 max: 15.2
setting NFos5 max: 18.8
setting NFos6 max: 49.8
setting NFos7 max: 77.5
setting NFos8 max: 51.6
setting NFos9 max: 16.8
preorder prep
calculating character durations
setting min and max
setting up all constraints
getting feasible start dates
start rate 0.0013070145
numparams:95
initial calc: 1e+15
problem initializing. trying again.
attempting to get feasible start rates/dates.
new start rate 0.0013573857
initial calc: 1e+15
problem initializing. trying again.
attempting to get feasible start rates/dates.
new start rate 0.0011756186
initial calc: 1e+15
problem initializing. trying again.
attempting to get feasible start rates/dates.
new start rate 0.0011923232
initial calc: 1e+15
problem initializing. trying again.
attempting to get feasible start rates/dates.
new start rate 0.0011704216
initial calc: 1e+15
problem initializing. trying again.
attempting to get feasible start rates/dates.
new start rate 0.001218504
initial calc: 1e+15
problem initializing. trying again.
attempting to get feasible start rates/dates.
new start rate 0.0011420022
initial calc: 1e+15
problem initializing. trying again.
attempting to get feasible start rates/dates.
new start rate 0.0014572266
initial calc: 1e+15
problem initializing. trying again.
attempting to get feasible start rates/dates.
new start rate 0.001355159
initial calc: 1e+15
problem initializing. trying again.
attempting to get feasible start rates/dates.
new start rate 0.0015092535
initial calc: 1e+15
problem initializing. trying again.
attempting to get feasible start rates/dates.
new start rate 0.0013136115
initial calc: 1e+15
Failed setting feasible start rates/dates after 10 attempts. Aborting.

We would be very keen to understand better what is going wrong here and
what we might be able to do about it, so that we can use treePL somewhat
reliably in a pipeline where a variety of topologies/branch
lengths/calibration points are going to be thrown at it. Some possible
directions that might work include:

• maybe try more attempts? There's probably still going to be
  situations that will then just result in an infinite loop so perhaps not a
  general solution.
• us getting a better understanding of which combinations of
  calibration points can have this effect so that we can make our adjustments
  to the input before submitting it to treePL
• treePL itself being able to detect combinations of calibration
  points that will have this effect and somehow making adjustments on the fly
• or maybe we should modify our input files in ways we are not aware
  of?

Thanks! Hope you're not getting tired of my issues :)

Rutger

—
Reply to this email directly or view it on GitHub
#16.

[rvosa]

Aha! But that is already very useful information, stupid I didn't notice that. As you must be able to guess: we have a situation where a single set of calibration points is applied to a whole bunch of trees (either from mcmc or bootstrapping). The calibration points are defined with reference to higher taxa, for which we first lookup all the putative members, then get the MRCA, then get all the real members, and stick that in our treePL input file. If the trees are incompatible with the taxonomy then of course it can happen that what are supposed to be distinct calibration points end up on top of each other. Oops. I guess on our end this means that we should figure out which of the points on top of each other are closer to the "correct" one (I guess: the oldest one) and try that. But a little warning in treePL would be pretty good too. Thanks! Does our command file otherwise make sense?

[rvosa]

So we now have a fair workaround for this thanks to your sharp eye. As far as we're concerned this means you can close this issue - unless you still want to keep this open to remind yourself about some warnings that you would like treePL to issue. Thanks a lot!

[blackrim]

Sounds good. I will leave it here for a bit as a reminder.
Thanks
On Fri, May 29, 2015 at 09:00:11AM -0700, Rutger Vos wrote:

So we now have a fair workaround for this thanks to your sharp eye. As far as we're concerned this means you can close this issue - unless you still want to keep this open to remind yourself about some warnings that you would like treePL to issue. Thanks a lot!

---

Reply to this email directly or view it on GitHub:
#16 (comment)

[mckelvyad]

Hi all,
I'm having a similar problem but I'm not sure which part of my file is causing it. Do you only need the first and last taxa in the group, or must you name all taxa for treePL to be able to make sense of groups? The tree I'm trying to use is rather large.
Thanks!
Alex

[josephwb]

You only need two tips to define a mrca.
JWB

On 10 November 2015 at 17:42, mckelvyad [email protected] wrote:

Hi all,
I'm having a similar problem but I'm not sure which part of my file is
causing it. Do you only need the first and last taxa in the group, or must
you name all taxa for treePL to be able to make sense of groups? The tree
I'm trying to use is rather large.
Thanks!
Alex

—
Reply to this email directly or view it on GitHub
#16 (comment).

[mckelvyad]

Thanks, that's what I thought. I guess I will share the full info, hopefully that will help. I'm sure it's something similar to the OP that I must have overlooked. If the following can be easily formatted to not all be jumbled together, let me know how and I'll edit it. Sorry for how messy it looks, I'm not familiar with github's formatting. Anyway, thanks in advance!

Config file:
treefile = arbfinal.tre smooth = 100 numsites = 9523 mrca = Aniliidae Anilius_scytale Trachyboa_boulengeri mrca = Charinidae Lichanura_trivirgata Charina_umbratica mrca = Colubrinae Grayia_ornata Coelognathus_radiatus mrca = PanSerpentes Liotyphlops_albirostris Pseustes_poecilonotus_7_AMNH_152285 mrca = Corallus Corallus_batesii Corallus_cookii mrca = Colubroidea Xenodermus_javanicus Acrochordus_javanicus mrca = Eunectes Eunectes_notaeus Eunectes_murinus mrca = Charininae Charina_bottae Charina_umbratica mrca = Alethinophidia Liotyphlops_albirostris Anilius_scytale mrca = Natricinae Aspidura_trachyprocta Plagiopholis_styani mrca = Morelia Morelia_viridis Morelia_spilota mrca = Loxocemidae Loxocemus_bicolor Xenopeltis_unicolor mrca = Xenodontinae Heterodon_platirhinos Psomophis_obtusus mrca = Caenophidia Acrochordus_javanicus Casarea_dussumieri mrca = Elapidae Calliophis_melanurus Pythonodipsas_carinata mrca = Viperidae Causus_resimus Aplopeltura_boa mrca = Boinae Boa_constrictor Chilabothrus_angulifer min = Aniliidae 72.1 max = Aniliidae 72.1 min = Charinidae 35.2 max = Charinidae 35.2 min = Colubrinae 11.1 max = Colubrinae 12.75 min = PanSerpentes 98.3 max = PanSerpentes 113 min = Corallus 50.2 max = Corallus 64 min = Colubroidea 13.6 max = Colubroidea 15.97 min = Eunectes 12.4 max = Eunectes 12.4 min = Charininae 18.7 max = Charininae 18.7 min = Alethinophidia 93.9 max = Alethinophidia 100.5 min = Natricinae 10.3 max = Natricinae 13.6 min = Morelia 12.5 max = Morelia 12.5 min = Loxocemidae 35.2 max = Loxocemidae 35.2 min = Xenodontinae 4.9 max = Xenodontinae 13.6 min = Caenophidia 48.6 max = Caenophidia 55.8 min = Elapidae 12.75 max = Elapidae 16.9 min = Viperidae 20 max = Viperidae 22.4 min = Boinae 58 max = Boinae 64 outfile = optimizeXX thorough prime nthreads = 4

Tree:XXXX - was wrong`

Error:
outfile: optimizeXX set thorough: true (MAY TAKE A WHILE) PRIMING the optimization parameters and then exiting setting the maximum number of threads to 4 finished reading config file using system clock for random number seed = 1447193742 tiny branch length at internal node. setting to 0.00010500893 setting Alethinophidia min: 93.9 setting Aniliidae min: 72.1 setting Boinae min: 58 setting Caenophidia min: 48.6 setting Charinidae min: 35.2 setting Charininae min: 18.7 setting Colubrinae min: 11.1 setting Colubroidea min: 13.6 setting Corallus min: 50.2 setting Elapidae min: 12.75 setting Eunectes min: 12.4 setting Loxocemidae min: 35.2 setting Morelia min: 12.5 setting Natricinae min: 10.3 setting Viperidae min: 20 setting Xenodontinae min: 4.9 setting Alethinophidia max: 100.5 setting Aniliidae max: 72.1 setting Boinae max: 64 setting Caenophidia max: 55.8 setting Charinidae max: 35.2 setting Charininae max: 18.7 setting Colubrinae max: 12.75 setting Colubroidea max: 15.97 setting Corallus max: 64 setting Elapidae max: 16.9 setting Eunectes max: 12.4 setting Loxocemidae max: 35.2 setting Morelia max: 12.5 setting Natricinae max: 13.6 setting Viperidae max: 22.4 setting Xenodontinae max: 13.6 preorder prep calculating character durations setting min and max setting up all constraints getting feasible start dates start rate 1.768914 numparams:1732 initial calc: 1e+15 problem initializing. trying again. attempting to get feasible start rates/dates. new start rate 1.5961779 initial calc: 1e+15 problem initializing. trying again. attempting to get feasible start rates/dates. new start rate 1.6445766 initial calc: 1e+15 problem initializing. trying again. attempting to get feasible start rates/dates. new start rate 1.6846419 initial calc: 1e+15 problem initializing. trying again. attempting to get feasible start rates/dates. new start rate 1.5033228 initial calc: 1e+15 problem initializing. trying again. attempting to get feasible start rates/dates. new start rate 1.7020864 initial calc: 1e+15 problem initializing. trying again. attempting to get feasible start rates/dates. new start rate 1.7301799 initial calc: 1e+15 problem initializing. trying again. attempting to get feasible start rates/dates. new start rate 1.683281 initial calc: 1e+15 problem initializing. trying again. attempting to get feasible start rates/dates. new start rate 1.5798622 initial calc: 1e+15 problem initializing. trying again. attempting to get feasible start rates/dates. new start rate 1.744816 initial calc: 1e+15 problem initializing. trying again. attempting to get feasible start rates/dates. new start rate 1.6947592 initial calc: 1e+15 Failed setting feasible start rates/dates after 10 attempts. Aborting.

[josephwb]

Are you sure that is the right config/tree? I get this error when trying to run it:

problem with taxa for mrca PanSerpentes = Pseustes_poecilonotus_7_AMNH_152285 doesn't exist 

[mckelvyad]

Yeah it's alright. Working on it now, we were able to get it running by removing a few calibrations. I can't attach the files here because of the extensions. Thank you guys for the help, I may have partly just needed to talk it out. Did I paste the wrong tree? Maybe, sorry. The name on the last one got switched up. Working in virtualbox and the version got messed up. This should be the correct one:

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009)76:2.146208)100:2.867063)99:2.860108)89:2.85497)91:2.853187)41:2.853422)100:2.862632)24:2.854928)85:2.857249)100:3.041245,((Liopeltis_frenatus_CAS225548:3.301801,(((Ptyas_mucosa:4.659206,(Ptyas_carinata_91_LSUHC10004:4.163175,Ptyas_carinata_92_LSUHC7600:2.826913)100:3.017175)100:3.023922,(Cyclophiops_major:4.249747,(Ptyas_dhumnades:5.142348,(Ptyas_nigromarginata_CAS236202:3.964227,Ptyas_nigromarginata_CAS241947:3.947503)96:4.094338)78:4.151129)99:1.958691)19:1.746498,(((Cyclophiops_multicinctus_FMNH255569:2.841838,Cyclophiops_multicinctus_AMNH153707:2.823081)99:3.007812,(Cyclophiops_multicinctus:4.160849,Cyclophiops_multicinctus_KU291939:3.025318)87:1.734893)100:1.754733,((Ptyas_fusca_ADM0006:2.840304,Ptyas_fusca_FMNH269019:2.846247)100:2.819515,(Ptyas_luzonensis:5.327489,(Ptyas_luzonensis_KU330134:4.141416,Ptyas_luzonensis_KU329295:4.0043)97:2.809422)100:2.829999)95:3.013361)100:1.942153)95:1.742004)97:1.741491,(((Dendrophidion_percarinatum:5.344904,(Drymobius_rhombifer:4.986755,(Dendrophidion_dendrophis:5.370236,(Dendrophidion_percarinatum_MVZ204098:3.632553,Dendrophidion_percarinatum_MVZ204099:5.347716)100:3.63704)4:3.804352)44:3.625417)100:3.638398,(((Oxybelis_fulgidus:6.014873,Oxybelis_aeneus:5.692231)99:5.834426,((Leptophis_depressirostris_YPM016868:5.231314,Leptophis_depressirostris_LSUMNS146385:5.145054)98:4.935908,(Leptophis_diplotropis_LSUMNS6328:3.663466,Leptophis_ahaetulla:5.810298)7:3.627521)100:3.625737)97:2.566969,((Opheodrys_aestivus:5.653805,Opheodrys_vernalis:5.654108)100:6.426115,(((Chironius_fuscus_KU214847:3.856101,Chironius_fuscus_LSUMNS13875:3.65048)100:3.803452,(Chironius_laevicollis:4.991323,(Chironius_scurrulus_LSUMNS9368:4.183067,(Chironius_scurrulus:4.180927,(Chironius_scurrulus_LSUMNS8940:2.820791,Chironius_scurrulus_AMNH152263:2.821981)83:3.799353)87:3.61805)33:3.624089)99:3.629336)99:2.561634,(Chironius_grandisquamis:5.038756,(((Chironius_flavolineatus:4.349723,(Chironius_monticola_AMNH150692:3.019531,Chironius_quadricarinatus:4.348833)76:3.614315)88:3.626312,(Chironius_monticola:5.394009,(Chironius_bicarinatus:5.032452,(Chironius_fuscus:5.031608,(Chironius_exoletus_AMNH152259:3.025118,Chironius_exoletus:4.213291)88:3.619388)97:2.801089)30:2.798955)98:3.623979)94:2.556661,((Chironius_carinatus:5.773742,(Chironius_multiventris_YPM016079:3.185448,Chironius_multiventris_YPM016080:2.821839)100:3.81155)99:3.623066,((Chironius_laurenti:5.695505,Chironius_multiventris_LSUMNS12556:2.9958)85:3.618583,((Chironius_multiventris:5.610363,Chironius_foveatus:4.863996)0:6.133897,(Chironius_exoletus_LSUMNS16518:4.143998,Chironius_multiventris_LSUMNS17665:2.821578)100:3.791493)89:2.801814)100:2.567695)100:2.56349)93:2.553861)81:2.554288)100:2.566233)66:2.557221)97:3.616736)94:3.849507,((Drymarchon_corais:5.654621,Drymarchon_couperi:6.272733)100:6.077418,((((Conopsis_biserialis:6.39248,Conophis_vittatus:6.391159)100:5.587507,(Pseudoficimia_frontalis:5.595117,Sympholis_lippiens:5.595791)94:5.573924)100:5.971082,(((Tantilla_relicta:5.632244,Tantilla_coronata:5.63647)100:5.586032,((Tantilla_gracilis:5.631462,Tantilla_hobartsmithi:5.629941)99:5.564542,(Tantilla_nigriceps:5.643308,Tantilla_planiceps:5.638488)74:5.553237)96:5.566083)100:6.041829,(Stenorrhina_freminvillei:5.814299,((Chionactis_occipitalis:5.796583,(Sonora_semiannulata:2.906277,Sonora_aemula:4.526669)54:2.858286)97:2.886243,(Chilomeniscus_stramineus:6.618842,(Sonora_michoacanensis:4.58504,Sonora_mutabilis:4.593991)100:4.495873)47:4.605467)96:3.021878)97:2.891693)17:2.856959)97:3.465102,((Tantilla_melanocephala:5.115123,((Coluber_schotti:5.844828,Coluber_taeniatus:5.649658)99:6.290813,(Coluber_lateralis:6.448914,(Coluber_flagellum:5.800868,(Coluber_bilineatus:6.027847,Coluber_constrictor:2.903888)60:2.855543)75:2.868948)6:2.855707)81:2.859915)95:1.940501,(((Rhinobothryum_lentiginosum:6.903961,(Salvadora_mexicana:6.587208,Salvadora_grahamiae:6.437837)89:6.970898)16:7.127212,((Drymoluber_dichrous:5.612189,Drymoluber_brazili:5.976525)96:5.586466,(Mastigodryas_bifossatus:6.863577,(Mastigodryas_melanolomus:7.095566,Mastigodryas_boddaerti:6.40255)0:6.465227)97:7.123463)100:5.585737)88:5.971709,(((Phyllorhynchus_decurtatus:2.25506,Phyllorhynchus_browni:6.199294)100:2.455203,(Salvadora_hexalepis:6.187928,Trimorphodon_biscutatus:2.912702)0:3.53264)97:1.312826,((Spilotes_pullatus:4.872831,Spilotes_pullatus_ADM259:5.053512)100:5.039159,((Spilotes_sulphureus:5.252427,(Phrynonax_shropshirei_LSUMNS7806:5.59652,(Spilotes_sulphureus_LSUMNS14023:4.770156,Spilotes_sulphureus_LSUMNS8937:4.771115)98:4.741018)98:4.927724)100:4.973041,((Phrynonax_poecilonotus:5.462866,Phrynonax_poecilonotus_ADM0005:3.651333)95:3.622789,(Phrynonax_shropshirei_LSUMNS7085:5.35032,(Phrynonax_polylepis:6.27915,Phrynonax_poecilonotus_AMNH152285:3.659043)0:3.623136)0:3.616337)100:3.830741)57:3.622041)92:3.836293)31:0.03033)22:0.01251)50:0.008814)31:0.001459)100:0.009635)98:0.004403)99:0.005709)95:0.002607)97:0.00306)100:0.021425)95:0.005331)99:0.01161)100:0.01817)100:0.029122)100:0.062638)98:0.027708)100:0.044186)100:0.006997)100:0.0554)100:0.247644)27:0.020352)100;'

Here's the working full config file:
'treefile = arbfinal.tre
smooth = 100
numsites = 9523
mrca = PanSerpentes Liotyphlops_albirostris Phrynonax_poecilonotus_AMNH152285
min = PanSerpentes 98.3
max = PanSerpentes 113
mrca = Aniliidae Anilius_scytale Trachyboa_boulengeri
min = Aniliidae 72.1
max = Aniliidae 72.1
mrca = Charinidae Lichanura_trivirgata Charina_umbratica
min = Charinidae 35.2
max = Charinidae 35.2
mrca = Charininae Charina_bottae Charina_umbratica
min = Charininae 18.7
max = Charininae 18.7
mrca = Boinae Boa_constrictor Chilabothrus_angulifer
min = Boinae 58
max = Boinae 64
mrca = Corallus Corallus_batesii Corallus_cookii
min = Corallus 50.2
max = Corallus 64
mrca = Eunectes Eunectes_notaeus Eunectes_murinus
min = Eunectes 12.4
max = Eunectes 12.4
mrca = Loxocemidae Loxocemus_bicolor Python_regius
min = Loxocemidae 35.2
max = Loxocemidae 35.2
mrca = Morelia Morelia_carinata Morelia_spilota
min = Morelia 12.5
max = Morelia 12.5
mrca = Alethinophidia Anilius_scytale Casarea_dussumieri
min = Alethinophidia 93.9
max = Alethinophidia 100.5
mrca = Caenophidia Acrochordus_javanicus Xenodermus_javanicus
min = Caenophidia 48.6
max = Caenophidia 55.8
mrca = Viperidae Proatheris_superciliaris Calloselasma_rhodostoma
min = Viperidae 20
max = Viperidae 22.4
mrca = Elapidae Calliophis_melanurus Ophiophagus_hannah
min = Elapidae 12.75
max = Elapidae 16.9
mrca = Natricinae Macropisthodon_rudis Aspidura_trachyprocta
min = Natricinae 10.3
max = Natricinae 13.6
mrca = Xenodontinae Diadophis_punctatus Pliocercus_elapoides
min = Xenodontinae 4.9
max = Xenodontinae 13.6
mrca = Colubrinae Oligodon_arnensis Coelognathus_radiatus
min = Colubrinae 11.1
max = Colubrinae 12.75
outfile = optimizeXX.tre
thorough
nthreads = 4
opt = 4
optad = 1
optcvad = 0
cv
cvoutfile = SuchAWellRoundedCV'

[josephwb]

Ok, good.
Was it an issue of conflicting constraints?

[mckelvyad]

It was! Thanks, especially for the quick replies!

[josephwb]

Okay, good to know. I think this thread has inspired a more thorough checking (and reporting) of the constraints.

[jamie-thompson]

Hi,

I have this problem, but not when I misspecified numsites. The constraints work fine when misspecified but not when correct.

Jamie