No mcmctree.log output

[kianayoon]

Hi there,

I have been testing out the new IQ2MC workflow and all seems to be running smoothly except I receive no mcmc.log output to be examined in Tracer after running mcmctree.
My two commands were:

iqtree3 -s pops80_clust95.phy -m TVMe+I -te pops80_clust95.nwk --dating mcmctree —mcmc-iter 2000, 2000, 200000 —mcmc-clock IND
mcmctree pops80_clust95.phy.mcmctree.ctl

Another smaller note: I had to manually replace the commas generated for 'BDparas' and replace them with spaces for it to run properly.

Here's the folder for the analysis.

Thanks for your support!

[piyumalanthony]

Hi @kianayoon,

Thanks for the comments!

We have fixed this issue in IQ-TREE 3, and the new fixes are available in https://github.com/iqtree/iqtree3/tree/master.

We will release these updates soon in the new IQ-TREE release.

Here, I have attached IQ-TREE 3 builds for your reference, which include all the fixes.

iqtree-3.0.1-Linux.tar.gz
iqtree-3.0.1-macOS.zip
iqtree-3.0.1-Windows.zip

[MatteoSebastianelli]

Hello,

I jump on this thread since I am basically experiencing a similar issue, though I am already uysing iqtree3 to generate the control file.

Below I paste the commands I am using to date my tree

iqtree=/crex/proj/snic2020-2-19/private/darwins_finches/users/seba/BIN/iqtree-3.0.1-Linux/bin
mcmctree=/crex/proj/snic2020-2-19/private/darwins_finches/users/seba/BIN/paml/bin/mcmctree

$iqtree/iqtree3 -s 

../finches_highcov_463_AllChr_QF_setGT_snps_biall_maxmiss075_maf003_DP2_100_phased_AA_beakLociRm_LDpruned_simplified.recode.min4.phy -m TEST -te finches_highcov_463_AllChr_QF_setGT_snps_biall_maxmiss075_maf003_DP2_100_phased_AA_beakLociRm_LDpruned_simplified_rooted.nwk --dating mcmctree --prefix finches_highcov_463_beakLociRm_LDpruned_simplified -T AUTO

cd ./run1
$mcmctree/mcmctree finches_highcov_463_beakLociRm_LDpruned_simplified.mcmctree.ctl

When I run the mcmctree command the only message I get is:

MCMCTREE in paml version 4.10.9, 7 May 2025

Reading options from finches_highcov_463_beakLociRm_LDpruned_simplified.mcmctree.ctl..

option ckpfile in finches_highcov_463_beakLociRm_LDpruned_simplified.mcmctree.ctl

I get no output except for the SeedUsed file.

Could you help me to figure out what have I been doing wrong? I attach the folder I have been workin on with mcmctree files for simplicity.

tree_dating.zip

Thank you in advance!

Matteo Sebastianelli

[piyumalanthony]

Hi @MatteoSebastianelli,

I try to check with your alignment and tree file but I cannot find the alignment (.phy file) in the attachment. Can you try the iqtree3 binaries attached in above with this thread which should work. You can simply use these iqtree3 binaries instead of current iqitree3 release which has issues with ctl file. The generated Hessian seems to be correct but there is missing argument in the ctl file for MCMCtree. The ctl file should look like the following, if you use the iqtree3 binaries attached above in the thread, you should get the correct control file. (The binaries from current iqtree3 release generate ctl file without print option and the BD params should not have commas.)

Also, since you are using IQ2MC pipeline, you should download MCMCtree binary from here: https://github.com/iqtree/paml/releases/tag/Latest

Otherwise, MCMCtree cannot identify newly introduced options under IQ2MC. If you use MCMCtree from original PAML package , you can simply use the original ctl file format in PAML package and discard the ctl file generated by iqtree3. Also, note that to run MCMCtree, you need to add fossil calibrations to your tree file. Currently a calibration is required for root as well.

Here, the error you are getting "option ckpfile in finches_highcov_463_beakLociRm_LDpruned_simplified.mcmctree.ctl" is due to the usage of MCMCtree binary which was taken from PAML package. If you download MCMCtree from here, you will not get this error.

Thank you!

[MatteoSebastianelli]

Dear @piyumalanthony ,

thank you for helping. It is now working.

All the best,
Matteo

[aureliendejode]

Hello,

I have a similar issue but I think I am using the latest version...

I am using mcmctree iqtree version (MCMCTREE in paml version 4.10.8.iq2mc, November 2024).
I followed the iqtree3 tutorial to produce the hessian file (https://iqtree.github.io/doc/Dating)
Then I am running mcmctree on a slurm cluster using the attached script and .ctl file.

I do not get and .log file despite specifying it in the .ctl file.
Is that an expected behavior ? If yes then I guess the MCMC log of parameters to examine in Tracer is to be found somewhere else ?

Thanks for your help with this.

sabtch.sh

#!/bin/bash
#SBATCH -c 12
#SBATCH -J mcmctree # job name
#SBATCH -p long
#SBATCH --mem=50G
#SBATCH -q long  # queue long cannot be preempted
#SBATCH -e errors.%A # error file name in which %A is replaced by the job ID
#SBATCH -o output.%A # output file name in which %A is replaced by the job

MCMCTREE=/grps2/bmtitus/programs/paml-4.10.8.iq2mc-linux-x86_64/src/mcmctree

$MCMCTREE

.ctl file

seed = -1
seqfile = mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.charsets.dummy.phy  * A dummy alignment only allow to run MCMCtree
treefile = clean_tree.nwk  * Rooted newick tree with annotated fossil/tip dates
mcmcfile = mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.charsets.mcmctree.log  * MCMC log of parameters that can be examined in Tracer
outfile = mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.charsets.mcmctree.out  * Output of the summerized results of MCMCtree
ckpfile = mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.charsets.mcmctree.ckp  * Checkpoint file of MCMCtree
hessianfile = mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.charsets.mcmctree.hessian  * File with gradient and hessian matrix


checkpoint = 1 * 0: nothing; 1 : save; 2: resume
ndata = 328 * number of partitions
seqtype = 0    * 0 : nucleotides; 1: codons; 2: AAs (not required if the approximate likelihood method is used)
usedata = 1    * 0: sampling from priors with no data; 1: exact slow likelihood; 2: approximate likelihood
clock = 3     * 1: global clock with equal rates; 2: independent rates; 3: correlated rates

BDparas = 1,1,0.5    * birth rate, death rate, sampling priors for sampling times
finetune = 1 0.1  0.1  0.1  0.01 .5  * auto (0 or 1) : times, musigma2, rates, mixing, paras, FossilErrprint = 1  * 1: normal output; 2: verbose output

*** These parameters are used for multi-loci partitioned data (ndata > 1), see dos Reis et al .(2013)

rgene_gamma = 2 2     * alpha and beta parameter of Dirichlet-gamma prior for mean rate across loci for clock=2 or 3
sigma2_gamma = 1 10   * alpha and beta parameter of Dirichlet-gamma prior for rate variance across loci for clock=2 or 3

*** These parameters control the MCMC run

burnin = 5000
sampfreq =  5
nsample =  5000

***  Note: Total number of MCMC iterations will be burnin + (sampfreq * nsample)

***  Following parameters only needed to run MCMCtree with exact likelihood (usedata = 1), no need to change anything for approximate likelihood (usedata = 2)

model = 0      * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
alpha = 0      * 0: No rate heterogeneity across sites; otherwise: initial alpha parameter of the Gamma distribution
ncatG = 0      * Number of rate categories for the discrete Gamma distribution

cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?

kappa_gamma = 6 2      * gamma prior for kappa of the HKY model
alpha_gamma = 1 1       * alpha and beta parameter of Gamma distribution for heterogeneous rates across sites

[piyumalanthony]

Hi @aureliendejode,

Can you try the IQ-TREE version available here (#1 (comment)) in this thread to generate the Hessian and other files required for MCMCtree?

The IQ-TREE 3.0.1 version, which is available here has not been updated yet, and the version above should work and give correct behavior.

Thanks for reporting the issue!

[aureliendejode]

Thanks!
I used the version you provided and it worked.

I do have an additional question though:
In the control file produced by the iqtree3 cmd line, the usedata line is as follow:
usedata = 2 * 0: sampling from priors with no data; 1: exact slow likelihood; 2: approximate likelihood
When I run mcmctree with this I don' t get any results....
I get a log file but there are no values in it.

I changed it to:
usedata = 1 * 0: sampling from priors with no data; 1: exact slow likelihood; 2: approximate likelihood

Then, everything seems to works properly.

Is that expected behavior ? or am I missing something ?

Thanks for your help with this

[piyumalanthony]

Hi @aureliendejode,

Sorry for the late reply.

The behaviour you mentioned seems to be strange. The usedata = 2 option is to use the approximate likelihood method, and if you use usedata = 1, it will use the exact likelihood under the default substitution model. Therefore, it will not use the Hessian calculated under the previous step. Also, it should be very slow. Can you check if the Hessian is generated by IQ-TREE correctly before running MCMCtree?

If you can provide the log files here, it will be useful.

Thank you!

[aureliendejode]

Hi,
I attached the log file here and the beginning of the hessian file.
Thanks for your help

head *.hessian

66

((((((((((((((A_californica_Mex41a:0.0000021778,Actinostella_sp_nov_pan15_67a:0.0052170541)85.3/94:2.866227734e-06,Actinostella_flosculifera_ANT130:0.0000021861)99.7/100:2.17449822e-06,((A_californica_mex40a:0.0052170595,A_flosculifera_from_mexico_rg149b:0.0000025238)76.8/89:2.295293395e-06,A_flosculifera_from_Bocas_pan16_48:0.0000022643)100/100:2.183390986e-06)100/100:0.05274959609,((Actinostella_sp_ANT2:0.0156892144,Phymanthus_crucifer_ANT121:0.0307076955)100/100:2.69594845e-06,((((Heteractis_aurora_MDFBHA1:0.0000019796,Heteractis_aurora_MDKNHA2:0.0000021851)99.8/100:2.695283963e-06,Heteractis_aurora_MDKNHA3:0.0000026950)100/100:2.432863899e-06,(Macrodactyla_doraensis_MDOR1PHIL:0.0000026793,Macrodactyla_doreensis_K114:0.0000021104)100/100:0.009656784877)7.9/65:0.004803630359,(((Heteractis_crispa_HC02UAE:0.0047211443,Heteractis_crispa_HC1SI:0.0000023060)100/100:2.222751621e-06,((Heteractis_crispa_HC3MO5:0.0000027236,(Heteractis_malu_HMALU1TG:0.0000029087,Heteractis_malu_HMALU2TG:0.0000020228)100/100:2.247924545e-06)10.8/70:2.576044581e-06,Heteractis_crispa_PLHC516:0.0000025209)83.2/93:2.374723571e-06)100/100:0.004736625726,Heteractis_crispa_HC22RS:0.0047764266)100/100:2.537621101e-06)100/100:0.02111667815)100/100:0.02551132593)100/100:0.00505122887,(Actinioidea_sp_ANT126:0.0073961445,Anthopleura_sp_ANT131:0.0140555759)100/100:0.03284924535)100/100:0.01465500046,Bunodosoma_granuliferum_ANT211:0.0691950698)100/100:0.03824841718,((((Actinia_equina_ACT_21:0.0000027002,Isactinia_sp_ACT_20:0.1083772968)68.2/63:2.123937433e-06,Actinia_tenebrosa_ACT_12B:0.0000026283)100/65:2.175890894e-06,Actinia_equina_ANT203:0.0000024912)100/100:0.1140852954,antsola:0.0425581771)100/100:0.0146985792)100/100:0.09672323965,Isosicyonis_alba_ANT_10:0.0644960169)100/100:0.003589598859,((((((Cryptodendrum_adhaesivum_CA1GBR:0.0050892194,Cryptodendrum_adhaesivum_CA1MO:0.0000028473)100/100:2.09570839e-06,(Thalassianthus_hemprichii_THEMP1GBR:0.0000024219,Thalassianthus_hemprichii_THEMP2GBR:0.0000024124)100/100:0.005068930398)100/100:0.00541755565,(Stichodactyla_tapetum_STAP1GBR:0.0221329800,Stichodactyla_tapetum_STAP1VN:0.0157390111)100/100:0.01115975452)100/100:0.004866679578,(Stichodactyla_mertensii_PHILSHAD1:0.0000023526,(Stichodactyla_mertensii_SM2MD:0.0000026386,Stichodactyla_mertensii_SM30WIO:0.0000021505)99/100:2.221457118e-06)100/100:0.005101337626)100/100:2.23694949e-06,(((Heteractis_magnifica_HM1GBR:0.0049597101,Heteractis_magnifica_HM1MO1:0.0101503108)97.9/99:2.787283096e-06,(Heteractis_magnifica_HM2WIO:0.0000019976,Heteractis_magnifica_purple_ecomorph_MDFBHM1:0.0000021580)60.8/89:2.533572141e-06)100/100:0.01014313288,((((Stichodactyla_cf_haddoni_K123:0.0000027363,Stichodactyla_haddoni_K116:0.0000021087)99/100:2.296885949e-06,Stichodactyla_haddoni_K080:0.0000022611)100/100:2.222834081e-06,Stichodactyla_haddoni_SHADD1_SL:0.0000021470)100/100:2.070422031e-06,Stichodactyla_gigantea_SG1_GBR:0.0050908029)100/100:0.005074575167)98.8/98:2.663201362e-06)100/100:2.434036478e-06,((Stichodactyla_helianthus_ANT127:0.0000023655,Stichodactyla_helianthus_PANSH24:0.0000028409)99.8/100:2.03631542e-06,Stichodactyla_helianthus_PANSH48:0.0000024908)100/100:0.021212874)100/100:0.05495915805)100/100:0.01395888793,Bunodactis_octoradiata_ANT158:0.0775122081)99.8/100:2.27926128e-06,(((Entacmaea_quadricolor_EQ3SI:0.0000020349,Entacmaea_quadricolor_MAL16EQ4C:0.0000027014)20.4/73:2.916720868e-06,Entacmaea_quadricolor_K005EQ:0.0000025476)100/81:0.004841489714,Entacmaea_quadricolor_EQNTDAR1B:0.0000022442)100/100:0.09326616363)100/100:0.1092478733,(Actinostola_orange_ANT124:0.0029831449,Stomphia_didemon_ANT159:0.0190041544)100/100:0.1552800139)100/100:0.09609507301,((((Alicia_sansibaransis_ANT205:0.0410543449,Lebrunia_danae_ANT9:0.0751540722)100/100:0.02973758599,(Laviactis_lucida_ANT215:0.0096183626,exmask:0.0325606091)100/100:0.08423622729)100/100:0.1160500094,Antipodactis_awii_ANT208:0.0620102719)100/100:0.08062711352,Antholoba_achates_ANT206:0.1623875176)100/100:0.04873768985)100/100:0.09423241901,(Halcurias_pilatus_ANT4:0.0938022464,Synhalcurias_elegans_ANT221:0.1174280606)100/100:0.07625557809,nvmask:0.3946566995)100;

  0.0942324   0.0960951    0.109248 2.27926e-06   0.0139589   0.0035896   0.0967232   0.0382484    0.014655  0.00505123   0.0527496  2.1745e-06 2.86623e-06 2.17776e-06  0.00521705 2.18613e-06 2.18339e-06 2.29529e-06  0.00521706 2.52382e-06 2.26435e-06   0.0255113 2.69595e-06   0.0156892   0.0307077   0.0211167  0.00480363 2.43286e-06 2.69528e-06 1.97958e-06 2.18512e-06 2.69498e-06  0.00965678 2.67931e-06 2.11042e-06 2.53762e-06  0.00473663 2.22275e-06  0.00472114 2.30599e-06 2.37472e-06 2.57604e-06 2.72355e-06 2.24792e-06 2.90873e-06 2.02276e-06 2.52087e-06  0.00477643   0.0328492  0.00739614   0.0140556   0.0691951   0.0146986    0.114085 2.17589e-06 2.12394e-06 2.70016e-06    0.108377 2.62835e-06  2.4912e-06   0.0425582    0.064496   0.0549592 2.43404e-06 2.23695e-06  0.00486668  0.00541756 2.09571e-06  0.00508922 2.84727e-06  0.00506893 2.42191e-06 2.41243e-06   0.0111598    0.022133    0.015739  0.00510134 2.35261e-06 2.22146e-06 2.63864e-06 2.15055e-06  2.6632e-06   0.0101431 2.78728e-06  0.00495971   0.0101503 2.53357e-06 1.99757e-06 2.15798e-06  0.00507458 2.07042e-06 2.22283e-06 2.29689e-06  2.7363e-06 2.10866e-06 2.26115e-06 2.14699e-06   0.0050908   0.0212129 2.03632e-06 2.36551e-06 2.84091e-06 2.49085e-06   0.0775122   0.0932662  0.00484149 2.91672e-06 2.03492e-06 2.70138e-06 2.54763e-06 2.24425e-06     0.15528  0.00298314   0.0190042   0.0487377   0.0806271     0.11605   0.0297376   0.0410543   0.0751541   0.0842362  0.00961836   0.0325606   0.0620103    0.162388   0.0762556   0.0938022    0.117428    0.394657

  -0.0196953  -0.00106824   0.00213976     -18.1345   -0.0504043    0.0515023   0.00726022   0.00949443  0.000856554   0.00283721   0.00155362     -203.018     -203.018     -203.018  -0.00101622     -203.019     -203.018     -203.018  -0.00121294     -203.018     -203.019  0.000251765     -177.445 -0.000520418  -0.00403632  5.33566e-07  -0.00944271     -167.983     -210.178     -210.179     -210.179     -210.178  -0.00892861     -211.972     -211.972     -188.375  -0.00985011     -213.724  -0.00991863     -213.726     -213.726     -213.727     -213.727     -213.728     -213.727     -213.728     -213.727  -0.00900927 -0.000420954   0.00821624 -0.000301612   0.00485048    -0.043816   0.00126775     -205.647     -205.648     -205.648  0.000740701     -205.648     -205.647   -0.0141682   -0.0121004    0.0203663     -149.484     -179.382    0.0103746   0.00803935     -185.016   0.00788567      -198.14   0.00833741     -200.168     -200.168   0.00700881   0.00668811    0.0093784   0.00634585     -197.491     -197.491     -197.493     -197.493     -186.797   0.00858581     -191.844   0.00805988   0.00937987     -145.643     -202.735     -202.735   0.00936212     -192.759     -199.344     -199.344     -199.344     -199.344     -199.344     -199.344   0.00961436   0.00696522     -199.936     -139.861     -199.936     -199.936   0.00129477    0.0163533   -0.0116482     -208.118      -208.12      -208.12     -208.118     -113.998   0.00612977   -0.0621746   0.00226175    0.0128675    0.0188025  0.000953799   -0.0116024   -0.0162918   0.00279732   0.00196311   -0.0155185   0.00144222   0.00544693  -0.00403458    0.0105756   -0.0105686   0.00147612  -0.00468848

mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.charsets.log

[aureliendejode]

Hi,

I should add that I am trying to run this for a dataset with 328 partitions and I provided the alignment in phylip format and a .charsets file.
Do you an idea about what went wrong ?

Thanks for your hem with this

Best

[aureliendejode]

Hi,
I finally solved this!
Something went wrong on the first install I had on my HPC.
After reinstalling the proper version and compiling directly on the HPC it all worked well.
Best

[stephen-14]

Hi there,
I try to run IQ2MC, after estimating the Hessian for MCMC dating, I run the MCMCtree how ever, I encounterd this matter. I've tried to find the solution but seems no idea. Is there any body having the same issue?

iqtree -s speciestree_trim_0118.fa-out.phy -m VT+F+I+R5 -te Armophorea_time.nwk --dating mcmctree --mcmc-iter 20000,200,50000 --mcmc-bds 1,1,0.5 --mcmc-clock IND -nt AUTO

~/phylogeny/Time_scale/paml/src/mcmctree /home/biolab/phylogeny/new_time_tree/speciestree_trim_0118.fa-out.phy.mcmctree.ctl
MCMCTREE in paml version 4.10.10, 29 Jan 2026

Reading options from /home/biolab/phylogeny/new_time_tree/speciestree_trim_0118.fa-out.phy.mcmctree.ctl..

option ckpfile in /home/biolab/phylogeny/new_time_tree/speciestree_trim_0118.fa-out.phy.mcmctree.ctl

Thank you for your suport!

[piyumalanthony]

Hi @stephen-14,

Can you try latest version of IQ-TREE: https://github.com/iqtree/iqtree3/releases/tag/v3.1.0 and MCMCTree available here: https://github.com/iqtree/paml/releases/tag/Latest.

IQ2MC does not support the original PAML version, but the modified version, which I mentioned above. This should work fine.