before.log

	-> fasta load 
Loading the bamfile
The bam file Chr22_024_36_68_0097_eps10.sorted.MD.coord.bam has been inputted successfully
Reference is not provided, and it will be reconstructed according to the MD tags!
mapped_only: 0
We will focus on Chromosome chr22!
	-> Now at Chromosome: chr22

	[ALL done] cpu-time used =  0.01 sec
	[ALL done] walltime used =  0.00 sec

The misincorporting matrix is as follows:
Dir.	Pos.	FreqCT	FreqGA
5'	1	0.232472	0.000000
5'	2	0.145299	0.000000
5'	3	0.088353	0.000000
5'	4	0.071111	0.008621
5'	5	0.049808	0.000000
3'	1	0.000000	0.188976
3'	2	0.004274	0.149194
3'	3	0.004274	0.111111
3'	4	0.004274	0.052174
3'	5	0.000000	0.039216

The inference is under progress...
The fragment length distribution is calculated from the bam file!
The chosen model is non-biotin model.

	[ALL done] cpu-time used =  2.6879 sec
	[ALL done] walltime used =  2.0000 sec
The chosen model is non-biotin model, the inferred parameters are given as follows:
lambda: 0.348019 (0.300381,0.395657), delta: 0.008409 (0.004223,0.012595), delta_s: 0.730853 (0.595089,0.866617), nu: 0.004318 (-0.009951,0.018587), nfunctioncalls: 33 ngradientcalls: 33, llh: -4.633483.
	-> [read_all_reads] htsname: Chr22_024_36_68_0097_eps10.sorted.MD.coord.bam bedfile: chr22.bed
	-> Parsing possible bedfile: chr22.bed
ret.size(): 1000
mynSites: 100
mu_anc	sig_anc	mu_mod	sig_mod
60.000000	45.000000	100.000000	45.000000
lik[0,100]=605.903249
lik[100,200]=593.731696
lik[200,300]=576.227292
lik[300,400]=561.731197
lik[400,500]=575.352765
lik[500,600]=577.829750
lik[600,700]=573.036769
lik[700,800]=571.126075
lik[800,900]=572.369892
lik[900,1000]=603.281844
total lik[0,1000]: 5810.590528
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
60.000000	45.000000	100.000000	45.000000
lik[0,100]=605.903249
lik[100,200]=593.731696
lik[200,300]=576.227292
lik[300,400]=561.731197
lik[400,500]=575.352765
lik[500,600]=577.829750
lik[600,700]=573.036769
lik[700,800]=571.126075
lik[800,900]=572.369892
lik[900,1000]=603.281844
total lik[0,1000]: 5810.590528
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
41.867816	50.783145	103.981004	51.030449
lik[0,100]=603.414717
lik[100,200]=591.151224
lik[200,300]=574.001931
lik[300,400]=558.696645
lik[400,500]=573.938326
lik[500,600]=573.359338
lik[600,700]=571.375081
lik[700,800]=570.194587
lik[800,900]=569.134402
lik[900,1000]=599.025559
total lik[0,1000]: 5784.291810
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
31.251284	62.893690	114.621082	58.321631
lik[0,100]=603.409060
lik[100,200]=592.163942
lik[200,300]=573.418533
lik[300,400]=557.666476
lik[400,500]=571.371474
lik[500,600]=572.295011
lik[600,700]=569.395610
lik[700,800]=567.697606
lik[800,900]=568.022217
lik[900,1000]=599.097321
total lik[0,1000]: 5774.537251
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	59.434363	117.781278	60.309504
lik[0,100]=602.764613
lik[100,200]=591.237774
lik[200,300]=572.947131
lik[300,400]=557.215328
lik[400,500]=571.745937
lik[500,600]=571.583367
lik[600,700]=569.536491
lik[700,800]=568.173674
lik[800,900]=567.664806
lik[900,1000]=598.094080
total lik[0,1000]: 5770.963202
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	52.471073	127.476452	64.170974
lik[0,100]=601.935939
lik[100,200]=589.881985
lik[200,300]=572.337094
lik[300,400]=556.681946
lik[400,500]=572.956193
lik[500,600]=570.598124
lik[600,700]=570.255415
lik[700,800]=569.679130
lik[800,900]=567.570184
lik[900,1000]=596.552035
total lik[0,1000]: 5768.448045
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	53.060947	133.073626	65.603497
lik[0,100]=601.809403
lik[100,200]=589.907787
lik[200,300]=572.101835
lik[300,400]=556.443407
lik[400,500]=572.495987
lik[500,600]=570.406916
lik[600,700]=569.872541
lik[700,800]=569.217974
lik[800,900]=567.385741
lik[900,1000]=596.496732
total lik[0,1000]: 5766.138322
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	54.663610	149.000000	67.796350
lik[0,100]=601.571652
lik[100,200]=590.065502
lik[200,300]=571.561841
lik[300,400]=555.902729
lik[400,500]=571.377950
lik[500,600]=569.983840
lik[600,700]=568.951959
lik[700,800]=568.096590
lik[800,900]=567.000005
lik[900,1000]=596.431434
total lik[0,1000]: 5760.943501
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	54.601241	149.000000	66.183390
lik[0,100]=601.545186
lik[100,200]=590.055857
lik[200,300]=571.498445
lik[300,400]=555.844438
lik[400,500]=571.318763
lik[500,600]=569.922059
lik[600,700]=568.892978
lik[700,800]=568.041021
lik[800,900]=566.983157
lik[900,1000]=596.387681
total lik[0,1000]: 5760.489585
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	54.351765	149.000000	59.731547
lik[0,100]=601.420068
lik[100,200]=590.020217
lik[200,300]=571.203402
lik[300,400]=555.569593
lik[400,500]=571.030060
lik[500,600]=569.630557
lik[600,700]=568.609475
lik[700,800]=567.770889
lik[800,900]=566.898555
lik[900,1000]=596.188684
total lik[0,1000]: 5758.341500
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	53.353861	149.000000	33.924178
lik[0,100]=600.142514
lik[100,200]=589.912297
lik[200,300]=568.913548
lik[300,400]=553.263347
lik[400,500]=568.442977
lik[500,600]=567.108289
lik[600,700]=566.153158
lik[700,800]=565.517496
lik[800,900]=565.856776
lik[900,1000]=594.706559
total lik[0,1000]: 5740.016961
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	52.042102	149.000000	0.000000
lik[0,100]=610.420763
lik[100,200]=601.921940
lik[200,300]=588.279885
lik[300,400]=573.767851
lik[400,500]=590.864065
lik[500,600]=586.048185
lik[600,700]=587.522039
lik[700,800]=587.293546
lik[800,900]=581.086414
lik[900,1000]=610.343013
total lik[0,1000]: 5917.547700
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	53.103989	149.000000	27.462096
lik[0,100]=599.320059
lik[100,200]=589.770935
lik[200,300]=567.846760
lik[300,400]=552.128572
lik[400,500]=567.156550
lik[500,600]=565.862155
lik[600,700]=564.930279
lik[700,800]=564.529423
lik[800,900]=565.119567
lik[900,1000]=594.053350
total lik[0,1000]: 5730.717649
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	52.899317	149.000000	22.168951
lik[0,100]=598.337384
lik[100,200]=589.447719
lik[200,300]=566.674579
lik[300,400]=550.896492
lik[400,500]=565.742446
lik[500,600]=564.578568
lik[600,700]=563.607632
lik[700,800]=563.505206
lik[800,900]=564.185079
lik[900,1000]=593.418726
total lik[0,1000]: 5720.393831
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	52.734215	149.000000	17.899161
lik[0,100]=597.240385
lik[100,200]=588.873814
lik[200,300]=565.414176
lik[300,400]=549.614161
lik[400,500]=564.248650
lik[500,600]=563.349683
lik[600,700]=562.277011
lik[700,800]=562.414872
lik[800,900]=563.111695
lik[900,1000]=592.806905
total lik[0,1000]: 5709.351352
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	52.601615	149.000000	14.469907
lik[0,100]=596.029721
lik[100,200]=588.058840
lik[200,300]=564.080409
lik[300,400]=548.318969
lik[400,500]=562.733632
lik[500,600]=562.219960
lik[600,700]=561.045899
lik[700,800]=561.258903
lik[800,900]=561.960825
lik[900,1000]=592.121397
total lik[0,1000]: 5697.828554
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	52.495991	149.000000	11.738304
lik[0,100]=594.717766
lik[100,200]=587.134395
lik[200,300]=562.695402
lik[300,400]=547.050680
lik[400,500]=561.239504
lik[500,600]=561.253274
lik[600,700]=560.066274
lik[700,800]=560.168590
lik[800,900]=560.794122
lik[900,1000]=591.241460
total lik[0,1000]: 5686.361468
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	52.413046	149.000000	9.593216
lik[0,100]=593.367447
lik[100,200]=586.275314
lik[200,300]=561.335172
lik[300,400]=545.882027
lik[400,500]=559.782126
lik[500,600]=560.517634
lik[600,700]=559.429888
lik[700,800]=559.287418
lik[800,900]=559.679328
lik[900,1000]=590.177677
total lik[0,1000]: 5675.734032
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	52.227574	149.000000	4.796608
lik[0,100]=589.572638
lik[100,200]=584.298465
lik[200,300]=557.927021
lik[300,400]=543.263404
lik[400,500]=555.919656
lik[500,600]=559.576294
lik[600,700]=559.111851
lik[700,800]=557.409967
lik[800,900]=557.138008
lik[900,1000]=587.003665
total lik[0,1000]: 5651.220969
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	52.227574	149.000000	4.796608
lik[0,100]=589.572638
lik[100,200]=584.298465
lik[200,300]=557.927021
lik[300,400]=543.263404
lik[400,500]=555.919656
lik[500,600]=559.576294
lik[600,700]=559.111851
lik[700,800]=557.409967
lik[800,900]=557.138008
lik[900,1000]=587.003665
total lik[0,1000]: 5651.220969
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	35.944282	30.000000	0.000000
lik[0,100]=nan
lik[100,200]=nan
lik[200,300]=nan
lik[300,400]=nan
lik[400,500]=nan
lik[500,600]=nan
lik[600,700]=nan
lik[700,800]=nan
lik[800,900]=nan
lik[900,1000]=nan
total lik[0,1000]: nan
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	34.748833	123.080298	0.000000
lik[0,100]=644.186618
lik[100,200]=623.459576
lik[200,300]=622.203519
lik[300,400]=609.161685
lik[400,500]=637.821606
lik[500,600]=617.569879
lik[600,700]=630.178138
lik[700,800]=635.334698
lik[800,900]=613.436652
lik[900,1000]=635.115460
total lik[0,1000]: 6268.467831
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	44.367596	137.344224	2.639631
lik[0,100]=617.105768
lik[100,200]=601.497498
lik[200,300]=588.390306
lik[300,400]=572.966827
lik[400,500]=593.951538
lik[500,600]=582.196394
lik[600,700]=584.774793
lik[700,800]=590.363118
lik[800,900]=581.243613
lik[900,1000]=610.754980
total lik[0,1000]: 5923.244835
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	48.503962	143.478154	3.774755
lik[0,100]=590.283978
lik[100,200]=583.590735
lik[200,300]=557.005534
lik[300,400]=542.502034
lik[400,500]=556.517392
lik[500,600]=558.187174
lik[600,700]=559.566633
lik[700,800]=558.202877
lik[800,900]=556.334174
lik[900,1000]=586.258196
total lik[0,1000]: 5648.448727
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	51.020612	147.210163	4.465387
lik[0,100]=589.083121
lik[100,200]=583.639874
lik[200,300]=556.980688
lik[300,400]=542.393238
lik[400,500]=555.312412
lik[500,600]=558.697653
lik[600,700]=558.733170
lik[700,800]=557.012584
lik[800,900]=556.383636
lik[900,1000]=586.210863
total lik[0,1000]: 5644.447239
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	42.133940	134.367692	0.708256
lik[0,100]=624.160990
lik[100,200]=607.411297
lik[200,300]=599.400775
lik[300,400]=583.120604
lik[400,500]=603.428815
lik[500,600]=591.857999
lik[600,700]=591.288669
lik[700,800]=601.944141
lik[800,900]=591.354726
lik[900,1000]=617.589420
total lik[0,1000]: 6011.557436
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	47.349093	141.904310	2.913132
lik[0,100]=593.625669
lik[100,200]=585.193799
lik[200,300]=559.377281
lik[300,400]=545.350241
lik[400,500]=560.265353
lik[500,600]=560.393407
lik[600,700]=563.381440
lik[700,800]=561.599133
lik[800,900]=558.217675
lik[900,1000]=588.277818
total lik[0,1000]: 5675.681815
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	49.053665	144.367652	3.633796
lik[0,100]=589.036294
lik[100,200]=582.911541
lik[200,300]=555.848549
lik[300,400]=541.486068
lik[400,500]=554.951182
lik[500,600]=557.666617
lik[600,700]=558.860935
lik[700,800]=556.945084
lik[800,900]=555.487283
lik[900,1000]=585.320526
total lik[0,1000]: 5638.514079
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	48.895353	144.660358	3.115519
lik[0,100]=587.813792
lik[100,200]=581.956303
lik[200,300]=554.356252
lik[300,400]=540.207662
lik[400,500]=553.221304
lik[500,600]=556.896941
lik[600,700]=558.240427
lik[700,800]=555.733310
lik[800,900]=554.485590
lik[900,1000]=584.064246
total lik[0,1000]: 5626.975827
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	48.262105	145.831180	1.042414
lik[0,100]=583.180527
lik[100,200]=577.015326
lik[200,300]=549.275775
lik[300,400]=532.821945
lik[400,500]=543.780488
lik[500,600]=550.503733
lik[600,700]=552.317969
lik[700,800]=547.941291
lik[800,900]=550.015949
lik[900,1000]=577.693997
total lik[0,1000]: 5564.547001
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	47.885378	145.237115	0.000000
lik[0,100]=572.288675
lik[100,200]=568.006720
lik[200,300]=535.289974
lik[300,400]=526.870373
lik[400,500]=525.980753
lik[500,600]=537.695940
lik[600,700]=541.785770
lik[700,800]=532.817197
lik[800,900]=538.542657
lik[900,1000]=566.098456
total lik[0,1000]: 5445.376514
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	47.880623	145.237578	0.000000
lik[0,100]=572.288007
lik[100,200]=568.005637
lik[200,300]=535.289358
lik[300,400]=526.870471
lik[400,500]=525.981186
lik[500,600]=537.695323
lik[600,700]=541.787295
lik[700,800]=532.818732
lik[800,900]=538.542671
lik[900,1000]=566.097046
total lik[0,1000]: 5445.375725
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	47.861604	145.239427	0.000000
lik[0,100]=572.285346
lik[100,200]=568.001312
lik[200,300]=535.286903
lik[300,400]=526.870875
lik[400,500]=525.982928
lik[500,600]=537.692867
lik[600,700]=541.793412
lik[700,800]=532.824889
lik[800,900]=538.542737
lik[900,1000]=566.091414
total lik[0,1000]: 5445.372685
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	47.785526	145.246826	0.000000
lik[0,100]=572.274868
lik[100,200]=567.984160
lik[200,300]=535.277242
lik[300,400]=526.872690
lik[400,500]=525.990099
lik[500,600]=537.683203
lik[600,700]=541.818140
lik[700,800]=532.849783
lik[800,900]=538.543193
lik[900,1000]=566.069015
total lik[0,1000]: 5445.362394
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.000000	47.562493	145.268517	0.000000
lik[0,100]=572.245702
lik[100,200]=567.935248
lik[200,300]=535.250388
lik[300,400]=526.879861
lik[400,500]=526.012986
lik[500,600]=537.656385
lik[600,700]=541.893055
lik[700,800]=532.925224
lik[800,900]=538.546347
lik[900,1000]=566.004552
total lik[0,1000]: 5445.349748
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.025270	47.556422	145.269032	0.000000
lik[0,100]=572.245552
lik[100,200]=567.935138
lik[200,300]=535.249989
lik[300,400]=526.880016
lik[400,500]=526.012062
lik[500,600]=537.658287
lik[600,700]=541.891672
lik[700,800]=532.923252
lik[800,900]=538.547080
lik[900,1000]=566.006291
total lik[0,1000]: 5445.349339
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.126350	47.532135	145.271090	0.000000
lik[0,100]=572.244974
lik[100,200]=567.934717
lik[200,300]=535.248411
lik[300,400]=526.880657
lik[400,500]=526.008378
lik[500,600]=537.665924
lik[600,700]=541.886146
lik[700,800]=532.915372
lik[800,900]=538.550037
lik[900,1000]=566.013279
total lik[0,1000]: 5445.347896
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
30.927384	47.229456	145.298124	0.000000
lik[0,100]=572.226808
lik[100,200]=567.907951
lik[200,300]=535.223303
lik[300,400]=526.890429
lik[400,500]=525.991156
lik[500,600]=537.714956
lik[600,700]=541.880151
lik[700,800]=532.890730
lik[800,900]=538.576424
lik[900,1000]=566.038295
total lik[0,1000]: 5445.340203
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
31.537179	46.934561	145.324963	0.000000
lik[0,100]=572.204776
lik[100,200]=567.873473
lik[200,300]=535.196460
lik[300,400]=526.900785
lik[400,500]=525.984847
lik[500,600]=537.746255
lik[600,700]=541.897706
lik[700,800]=532.893832
lik[800,900]=538.598643
lik[900,1000]=566.039904
total lik[0,1000]: 5445.336682
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
31.694366	46.821388	145.335472	0.000000
lik[0,100]=572.194239
lik[100,200]=567.856301
lik[200,300]=535.185018
lik[300,400]=526.904979
lik[400,500]=525.987231
lik[500,600]=537.750301
lik[600,700]=541.915211
lik[700,800]=532.907581
lik[800,900]=538.605319
lik[900,1000]=566.029717
total lik[0,1000]: 5445.335898
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
mu_anc	sig_anc	mu_mod	sig_mod
31.677795	46.821279	145.335530	0.000000
lik[0,100]=572.193779
lik[100,200]=567.855438
lik[200,300]=535.184770
lik[300,400]=526.905005
lik[400,500]=525.988287
lik[500,600]=537.748499
lik[600,700]=541.917569
lik[700,800]=532.910347
lik[800,900]=538.604878
lik[900,1000]=566.027307
total lik[0,1000]: 5445.335880
lik_grad[0,100]
lik_grad[100,200]
lik_grad[200,300]
lik_grad[300,400]
lik_grad[400,500]
lik_grad[500,600]
lik_grad[600,700]
lik_grad[700,800]
lik_grad[800,900]
lik_grad[900,1000]
total lik_grad[0,1000]
lik_hess[0,100]
lik_hess[100,200]
lik_hess[200,300]
lik_hess[300,400]
lik_hess[400,500]
lik_hess[500,600]
lik_hess[600,700]
lik_hess[700,800]
lik_hess[800,900]
lik_hess[900,1000]
total lik_hess[0,1000]
mu_anc: 31.677795 (nan,nan), sigma_anc: 46.821279 (nan,nan), mu_mod: 145.335530 (nan,nan), sigma_mod: 0.000000 (nan,nan), nfunctioncalls: 596 ngradientcalls: 589, llh: -5445.335880.
print msg mapped_only: 0
Loading the bedfile chr22.bed ...
No meaningful chromosome name is provided, therefore we will focus on all provided chromosomes!
	-> Now at Chromosome: chr22