I am running IQ-TREE on a dataset of 160 samples with on average 2.1 millions reads on a genome of 310 Mb.

However, the software has been computing for one week now, and progress in the standard output are very slow. 

The last segment of the standard output are:

    Create initial parsimony tree by phylogenetic likelihood library (PLL)... 101.349 seconds Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Optimizing NNI: done in 37959.5 secs using 99.58% CPU Estimate model parameters (epsilon = 1.000)
    1. Initial log-likelihood: -28771040.770
    2. Current log-likelihood: -28771036.989
    3. Current log-likelihood: -28771033.633
    4. Current log-likelihood: -28771030.718
    5. Current log-likelihood: -28771028.173
    6. Current log-likelihood: -28771025.940
    7. Current log-likelihood: -28771023.982
    8. Current log-likelihood: -28771022.265
    9. Current log-likelihood: -28771020.758
    10. Current log-likelihood: -28771019.437
    11. Current log-likelihood: -28771018.277
    12. Current log-likelihood: -28771017.259 Optimal log-likelihood: -28771016.360 Rate parameters:  A-C: 0.99469  A-G: 2.56577  A-T: 1.06937  C-G: 0.76029  C-T: 2.56126  G-T: 1.00000 Base frequencies:  A: 0.254  C: 0.244  G: 0.245  T: 0.256 Proportion of invariable sites:
    0.000 Gamma shape alpha: 3.383 Parameters optimization took 12 rounds (9957.005 sec) Time for fast ML tree search: 101193.759 seconds
    
    NOTE: ModelFinder requires 214666 MB RAM! ModelFinder will test up to 484 DNA models (sample size: 4006362) ...  No. Model         -LnL      df  AIC          AICc         BIC   1  GTR+F         28847670.292 339
    57696018.584 57696018.642 57700494.535   2  GTR+F+I       28847652.995 340 57695985.990 57695986.047 57700475.144   3  GTR+F+G4     
    28771009.772 340 57542699.545 57542699.602 57547188.699   4  GTR+F+I+G4    28771010.076 341 57542702.152 57542702.210 57547204.509  5  GTR+F+R2      28587738.467 341 57176158.933 57176158.992
    57180661.291

Would anyone know if ModelFinder will effectively test 484 DNA models?





It took days to output these five tests. Is there any shortcut for the estimation of the right substitution model?

> I am running IQ-TREE on a dataset of 160 samples with on average 2.1 millions reads on a genome of 310 Mb.

Not quite sure what you mean based on the above explanation, but log-likelihood values tell me this is a monstrous alignment. Nothing will be done fast with large alignments.

If on top of that you have insufficient RAM and the program needs to swap a lot, this could take months. I may be able to offer better advice if you explain in greater detail what your exact alignment is, but either way it sounds like you need to rethink your strategy. That means starting from a smaller alignment, or using a generic substitution model with an alignment you have.