diCal-v1.3: -F ex/data.fasta -I ex/params.txt -n 4 -p 3+2+2+3 -t 2 -N 1
dataset: ex/data.fasta
parameter file: ex/params.txt
number of alleles: 4
mutation rate theta = 4Nmu: 0.01443
mutation matrix:
[0.5030000000000001, 0.08200000000000002, 0.31500000000000006, 0.10000000000000002]
[0.18581418581418582, 0.0019980019980019984, 0.15784215784215785, 0.6543456543456544]
[0.6533466533466533, 0.15784215784215783, 0.0, 0.1888111888111888]
[0.097, 0.303, 0.085, 0.515]
recombination rate rho = 4Nr: 0.01
number of parameters to estimate: 4
parameter pattern: 3+2+2+3
end time: 2.0
PAC method: LOL
Runtime: linear in d
HMM decoding: (0) none
number of EM iterations: 1
printing expected coalescent events: false
L = number of loci: 100000
d = number of discretization intervals: 10
n = number of haplotypes: 4
c = number of cores: 1
suggested JVM memory flag O(L*d*n*c): -Xmx2G
discretization times (units of 2N generations): [0.0, 0.05384615384615385, 0.09210526315789473, 0.14, 0.2, 0.2857142857142857, 0.4117647058823529, 0.6086956521739131, 1.0, 2.0]
initial population size scaling factors: [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]

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ITER=0
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calling E-step with sizes: [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
starting hap 0 in chrom 0
finished hap 0 : -3533.670991164484
starting hap 1 in chrom 0
finished hap 1 : -2768.2435032582134
starting hap 2 in chrom 0
finished hap 2 : -2573.3454770310336
starting hap 3 in chrom 0
finished hap 3 : -2675.1647849466867
E-step log likelihood: -11550.424756400418
calling M-step
final sizes: [0.9368317357310617, 0.9368317357310617, 0.9368317357310617, 0.8864176707987969, 0.8864176707987969, 0.9033351807520666, 0.9033351807520666, 0.9642333260940865, 0.9642333260940865, 0.9642333260940865]