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Cibiv / IQ-TREE

Efficient phylogenomic software by maximum likelihood
http://www.iqtree.org
GNU General Public License v2.0
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BUG: Numerical underflow for lh-derivative #223

Open anhong11 opened 2 years ago

anhong11 commented 2 years ago

I run IQ-Tree multicore version 2.1.3 COVID-edition for Linux 64-bit built Apr 21 2021 with the following cmd: iqtree2 -s used_outgrp.flt.snp.pop.cf -m GTR+P -nt AUTO -ntmax 14 -bb 1000 And I got the following error:

Empirical quantities.
Base frequencies:  A: 0.249  C: 0.250  G: 0.250  T: 0.250
Watterson's estimator of heterozygosity: 0.1289
--

WARNING: Numerical underflow for lh-derivative
PoMo with N=9 and GTR (Tavare, 1986) mutation model; Sampling method: Weighted binomial; 52 states in total;

--
Model parameters.
Mutation    rates:  A-C: 0.07766  A-G: 0.26390  A-T: 0.09786  C-G: 0.04964  C-T: 0.26380  G-T: 0.07746
Exchangeabilities:  A-C: 0.31012  A-G: 1.05557  A-T: 0.39109  C-G: 0.19854  C-T: 1.05430  G-T: 0.30956
Base frequencies:  A: 0.249  C: 0.250  G: 0.250  T: 0.250
Estimated heterozygosity: 0.1950
A slight overestimation is expected and an effect of weighted binomial sampling; see manual.
--
Empirical quantities.
Base frequencies:  A: 0.249  C: 0.250  G: 0.250  T: 0.250
Watterson's estimator of heterozygosity: 0.1289
--

WARNING: Numerical underflow for lh-derivative
ERROR: phylokernelnew.h:3268: double PhyloTree::computeLikelihoodFromBufferGenericSIMD() [VectorClass = Vec4d, FMA = true, SITE_MODEL = false]: Assertion `std::isfinite(tree_lh) && "Numerical underflow for lh-from-buffer"' failed.
ERROR: STACK TRACE FOR DEBUGGING:
ERROR: 
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
anhong11 commented 2 years ago

After try with --safe, I still get the error as:

WARNING: Numerical underflow for lh-derivative
ERROR: phylokernelnew.h:3268: double PhyloTree::computeLikelihoodFromBufferGenericSIMD() [VectorClass = Vec4d, FMA = true, SITE_MODEL = false]: Assertion `std::isfinite(tree_lh) && "Numerical underflow for lh-from-buffer"' failed.
ERROR: STACK TRACE FOR DEBUGGING:
ERROR: 
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: used_outgrp.flt.snp.pop2.cf.log
ERROR: ***    Alignment files (if possible)
/var/spool/slurmd/job24329042/slurm_script: line 4: 35674 Aborted                 iqtree2 -s used_outgrp.flt.snp.pop2.cf -m GTR+P --safe -nt AUTO -ntmax 14 -bb 1000