Frequent failure of optimization for free rates site model

[MichaelWoodhams]

When optimizing a +R model, the optimization reaches a hard limit of 99 iterations without having converged. For example:

./iqtree -s humanMito.fasta -te humanMito.tree -m K3P+FQ+R -pre temp -redo -v

(For this particular data set, this occurs on nearly all DNA models.)

Here is the tail end of the output. Note how the +R parameters are slowly migrating in one direction.
I've e-mailed the sample files to Minh.

96. Current log-likelihood: -29902.7686567944
    Optimizing +R4 model parameters by 2-BFGS,EM algorithm...
    Rate parameters: A-C: 1.0000000000 A-G: 28.2498690342 A-T: 0.9694407528 C-G: 0.9694407528 C-T: 28.2498690342 G-T: 1.0000000000
    Base frequencies: A: 0.2500000000 C: 0.2500000000 G: 0.2500000000 T: 0.2500000000
    Site proportion and rates: (0.3777956238,0.0001001047) (0.3661763981,0.0001537014) (0.2515053973,1.1868637281) (0.0045225808,27.0489558811)
97. Current log-likelihood: -29902.6767806495
    Optimizing +R4 model parameters by 2-BFGS,EM algorithm...
    Rate parameters: A-C: 1.0000000000 A-G: 28.2495458718 A-T: 0.9700523791 C-G: 0.9700523791 C-T: 28.2495458718 G-T: 1.0000000000
    Base frequencies: A: 0.2500000000 C: 0.2500000000 G: 0.2500000000 T: 0.2500000000
    Site proportion and rates: (0.3787780284,0.0001001047) (0.3671282716,0.0001322813) (0.2496048302,1.1952691030) (0.0044888698,27.1063560906)
98. Current log-likelihood: -29902.5845485122
    Optimizing +R4 model parameters by 2-BFGS,EM algorithm...
    Rate parameters: A-C: 1.0000000000 A-G: 28.2489362374 A-T: 0.9694762182 C-G: 0.9694762182 C-T: 28.2489362374 G-T: 1.0000000000
    Base frequencies: A: 0.2500000000 C: 0.2500000000 G: 0.2500000000 T: 0.2500000000
    Site proportion and rates: (0.3797570600,0.0001001047) (0.3680770166,0.0001139548) (0.2477101348,1.2038509379) (0.0044557886,27.1340971259)
99. Current log-likelihood: -29902.4926644145
    Optimal log-likelihood: -29902.4926644145
    Parameters optimization took 99 rounds (200.3325202390 sec)
    Best tree printed to temp.treefile
    BEST SCORE FOUND : -29902.4926644145
    Total tree length: 0.0546463944

Total number of iterations: 0
CPU time used for tree search: 0.0000070000 sec (0h:0m:0s)
Wall-clock time used for tree search: 0.0000067140 sec (0h:0m:0s)
Total CPU time used: 200.5198740000 sec (0h:3m:20s)
Total wall-clock time used: 200.4912709580 sec (0h:3m:20s)
Best tree printed to temp.treefile

Analysis results written to:
IQ-TREE report: temp.iqtree
Maximum-likelihood tree: temp.treefile
Screen log file: temp.log

Date and Time: Mon Aug 21 14:44:10 2017

humanMito.fasta.txt
humanMito.tree.txt

[bqminh]

You can increase the number of optimization rounds with -nparam option.

iqtree -s humanMito.fasta -te humanMito.tree -m K3P+FQ+R -pre temp -redo -seed 1 -nparam 1000 -v

Result in convergence after 159 rounds:

156. Current log-likelihood: -29899.184
157. Current log-likelihood: -29899.172
158. Current log-likelihood: -29899.161
159. Current log-likelihood: -29899.150
     Optimal log-likelihood: -29899.140
     Rate parameters: A-C: 1.00000 A-G: 28.04391 A-T: 0.96037 C-G: 0.96037 C-T: 28.04391 G-T: 1.00000
     Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
     Site proportion and rates: (0.408,0.000) (0.421,0.000) (0.168,4.505) (0.003,78.011)
     Parameters optimization took 159 rounds (12.135 sec)

Since this problem rarely occurs and it is not a bug, rather a heuristic. I will mark it as resolved.

Minh