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executable file
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#!/bin/bash
caffeinate python main_config_snp_parallel_automated_mut_rate.py -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_vcholerae_pwr3_nostrain29_noclones.yaml -p 0.917 -m 10000 -l 2831716
caffeinate python main_config_snp_parallel_automated_mut_rate.py -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_vcholerae_pwr2_nostrain29_noclones.yaml -p 0.917 -m 10000 -l 2831716
caffeinate python main_config_snp_parallel_automated_mut_rate.py -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_vcholerae_pwr1_nostrain29_noclones.yaml -p 0.917 -m 10000 -l 2831716
##############################################################################
#caffeinate recopops snps -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_campylojej_pwr1.75_nostrain42_noclones.yaml -rs 1 -u 0.00000015 -v 0 -l 2593107
#caffeinate recopops snps -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_campylojej_pwr1_nostrain42_noclones.yaml -rs 1 -u 0.00000015 -v 0 -l 2593107
#caffeinate recopops snps -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_campylojej_pwr2_nostrain42_noclones.yaml -rs 1 -u 0.00000009 -v 0 -l 2593107
#caffeinate recopops snps -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_campylojej_pwr1.5_nostrain42_noclones.yaml -rs 1 -u 0.00000012 -v 0 -l 2593107
# V cholerae, gen length = 2831716
# Campylojej, gen length = 1246329
# E coli, gen length = 2593107
# E fecalis, gen length = 2168460
# Staph epidermidis, gen length = 2064920
# V cholerae, frac inv sites = 0.9154
# Campylojej, frac inv sites = 0.9676191533939787
# E coli, frac inv sites = 0.9
# E fecalis, frac in sites = 1 - 0.036463979311304934 = 0.963536020688695
# Staph ep, frac in sites = 1 - 0.04787061968502412 = 0.9521293803149758
## with the what was called the effective mutation rate
#
#caffeinate recopops snps -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_vcholerae_pwr1_nostrain29_noclones.yaml -rs 1 -u 0.00000045 -v 0 -l 2831716
#caffeinate recopops snps -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_vcholerae_pwr2_nostrain29_noclones.yaml -rs 1 -u 0.00000035 -v 0 -l 2831716
#caffeinate recopops snps -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_vcholerae_pwr3_nostrain29_noclones.yaml -rs 1 -u 0.00000021 -v 0 -l 2831716
#
## with the what was called the effective mutation rate
#
#caffeinate recopops snps -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_vcholerae_pwr1_nostrain29_noclones.yaml -rs 1 -u 0.000026100000 -v 0 -l 2831716
#caffeinate recopops snps -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_vcholerae_pwr2_nostrain29_noclones.yaml -rs 1 -u 0.00002030000000 -v 0 -l 2831716
#caffeinate recopops snps -t p -f inputs/prob_matrices/coa_prob_matrix_from_dist_vcholerae_pwr3_nostrain29_noclones.yaml -rs 1 -u 0.000012180000 -v 0 -l 2831716