Eigen error when running inference on simulation

[jtourig]

Curious if you all have seen this type of error and what you think the cause might be:

Command line: cagee --cores 8 --infile ../simulation-output/single-sigma-test//sigma-100-sim-10/simulation.txt --tree /dev/fd/63 --output_prefix ../simulation-inference/single-sigma-test///sigma-100-sim-10/ 

Optimizer strategy: Broyden-Fletcher-Goldfarb-Shanno algorithm
Iterations: 300
Expansion: 2
Reflection: 1

Starting Search for Initial Parameter Values
Sigma^2:63.206200862281
Score (-lnL): 669.92253078672
Sigma^2:63.206200862281
Score (-lnL): 669.92253078672
Sigma^2:63.206264068482
Score (-lnL): 669.92239580608
Sigma^2:64.206200862281
Score (-lnL): 667.84965135348
Sigma^2:64.206265068482
Score (-lnL): 667.84952220022
Sigma^2:80.425494122227
Score (-lnL): 646.79420628809
Sigma^2:80.425574547721
Score (-lnL): 646.79414358252
Sigma^2:90.691013385241
Score (-lnL): 640.83409516153
Sigma^2:90.691104076254
Score (-lnL): 640.83405768388
Sigma^2:   102.26814912
Score (-lnL): 637.58671062594
Sigma^2:102.26825138815
Score (-lnL): 637.58669329326
Sigma^2: 110.3174710118
Score (-lnL): 636.68365479954
Sigma^2:110.31758132927
Score (-lnL): 636.68364804751
Sigma^2: 114.8674816973
Score (-lnL): 636.51451275731
Sigma^2:114.86759656478
Score (-lnL): 636.51451107778
Sigma^2:116.29560474726
Score (-lnL): 636.50292764769
Sigma^2:116.29572104287
Score (-lnL): 636.50292744672
Sigma^2: 116.4870206901
Score (-lnL): 636.50275692125
Sigma^2:116.48713717712
Score (-lnL): 636.50275691462

Completed 8 iterations
Time: 0H 0M 24S
Best match is:  116.4870206901
Final -lnL: 636.50275692125

19 values were attempted (0% rejected)

Inferring processes for Base model
Score (-lnL): 636.50275692125
Maximum possible lambda for this topology: 0.016666666666667
Starting reconstruction processes for Base model
Done!

cagee: /N/u/tourigny/Carbonate/.conda/envs/cagee/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:367: Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, 1>::operator()(Eigen::Index, Eigen::Index) [with Derived = Eigen::Matrix<double, -1, -1>; Eigen::DenseCoeffsBase<Derived, 1>::Scalar = double; Eigen::Index = long int]: Assertion `row >= 0 && row < rows() && col >= 0 && col < cols()' failed.
./run_simulation_inferences.bash: line 22: 21709 Aborted                 (core dumped)

Something to do with my Eigen installation? It's running within a conda environment up to now without issue.

[jtourig]

Base_family_likelihoods.txt Base_results.txt are written to the ouput but that's it before the error

[benfulton]

It's most likely just a bug. Is it reproducible? (Even if it is Eigen we should handle it better than that)

[benfulton]

I think this is due to the branch probabilities calculation on https://github.com/hahnlab/CAGEE/blob/main/src/transcript_reconstructor.cpp#L266 . We need to discuss with the group the best way to fix. I'll disable it in the meantime.