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