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after.log
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-> 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 = 2.6926 sec
[ALL done] walltime used = 3.0000 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 52.080769 149.000000 1.000000
lik[0,100]=610.678312
lik[100,200]=601.669631
lik[200,300]=587.842849
lik[300,400]=572.683741
lik[400,500]=590.353160
lik[500,600]=585.649293
lik[600,700]=583.551537
lik[700,800]=586.863995
lik[800,900]=580.746029
lik[900,1000]=609.991035
total lik[0,1000]: 5910.029582
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 52.712998 149.000000 17.350433
lik[0,100]=597.070940
lik[100,200]=588.768062
lik[200,300]=565.223877
lik[300,400]=549.425119
lik[400,500]=564.027433
lik[500,600]=563.177590
lik[600,700]=562.087919
lik[700,800]=562.248623
lik[800,900]=562.947236
lik[900,1000]=592.714746
total lik[0,1000]: 5707.691548
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 52.309633 149.000000 6.918790
lik[0,100]=591.246235
lik[100,200]=585.148986
lik[200,300]=559.315927
lik[300,400]=544.291675
lik[400,500]=557.549582
lik[500,600]=559.779094
lik[600,700]=559.005133
lik[700,800]=558.222167
lik[800,900]=558.047573
lik[900,1000]=588.367316
total lik[0,1000]: 5660.973687
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 52.309633 149.000000 6.918790
lik[0,100]=591.246235
lik[100,200]=585.148986
lik[200,300]=559.315927
lik[300,400]=544.291675
lik[400,500]=557.549582
lik[500,600]=559.779094
lik[600,700]=559.005133
lik[700,800]=558.222167
lik[800,900]=558.047573
lik[900,1000]=588.367316
total lik[0,1000]: 5660.973687
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 47.838455 149.000000 1.000000
lik[0,100]=612.527644
lik[100,200]=602.883666
lik[200,300]=590.845440
lik[300,400]=575.685453
lik[400,500]=595.269166
lik[500,600]=588.290537
lik[600,700]=587.518776
lik[700,800]=591.927684
lik[800,900]=583.536223
lik[900,1000]=611.647382
total lik[0,1000]: 5940.131971
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 50.298799 149.000000 4.256918
lik[0,100]=588.767809
lik[100,200]=583.639972
lik[200,300]=557.430959
lik[300,400]=542.797434
lik[400,500]=555.799403
lik[500,600]=559.286526
lik[600,700]=559.339355
lik[700,800]=557.733120
lik[800,900]=556.973025
lik[900,1000]=586.213281
total lik[0,1000]: 5647.980883
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 47.939881 143.402613 1.000000
lik[0,100]=591.073892
lik[100,200]=582.622309
lik[200,300]=555.080997
lik[300,400]=542.415394
lik[400,500]=555.156207
lik[500,600]=558.599356
lik[600,700]=562.622235
lik[700,800]=557.801106
lik[800,900]=557.131771
lik[900,1000]=584.924258
total lik[0,1000]: 5647.427526
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 50.244138 148.870297 4.181448
lik[0,100]=588.698349
lik[100,200]=583.578539
lik[200,300]=557.346993
lik[300,400]=542.716291
lik[400,500]=555.711140
lik[500,600]=559.226118
lik[600,700]=559.298087
lik[700,800]=557.674554
lik[800,900]=556.919303
lik[900,1000]=586.134758
total lik[0,1000]: 5647.304131
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 49.092010 146.136455 2.590724
lik[0,100]=586.185627
lik[100,200]=581.117391
lik[200,300]=553.605587
lik[300,400]=538.982967
lik[400,500]=551.496635
lik[500,600]=556.176364
lik[600,700]=556.821740
lik[700,800]=554.384708
lik[800,900]=554.333332
lik[900,1000]=582.976259
total lik[0,1000]: 5616.080610
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 48.347504 144.369845 1.562797
lik[0,100]=584.809868
lik[100,200]=578.179447
lik[200,300]=548.614025
lik[300,400]=534.371670
lik[400,500]=546.057062
lik[500,600]=552.152454
lik[600,700]=554.728622
lik[700,800]=549.896367
lik[800,900]=551.012894
lik[900,1000]=579.193757
total lik[0,1000]: 5579.016168
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 48.139862 144.043783 1.000000
lik[0,100]=584.569322
lik[100,200]=577.588569
lik[200,300]=548.071682
lik[300,400]=533.891265
lik[400,500]=544.993663
lik[500,600]=551.348535
lik[600,700]=555.269681
lik[700,800]=549.041742
lik[800,900]=550.760512
lik[900,1000]=578.432647
total lik[0,1000]: 5573.967617
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 48.256786 144.227391 1.316915
lik[0,100]=584.505305
lik[100,200]=577.625175
lik[200,300]=547.836838
lik[300,400]=533.588832
lik[400,500]=545.001605
lik[500,600]=551.377645
lik[600,700]=554.672087
lik[700,800]=549.014705
lik[800,900]=550.589852
lik[900,1000]=578.479725
total lik[0,1000]: 5572.691770
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 41.305769 144.772594 1.000000
lik[0,100]=581.533896
lik[100,200]=574.620355
lik[200,300]=544.990771
lik[300,400]=529.399162
lik[400,500]=541.911299
lik[500,600]=547.999819
lik[600,700]=555.000892
lik[700,800]=548.742609
lik[800,900]=548.964788
lik[900,1000]=574.087537
total lik[0,1000]: 5547.251128
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
39.811615 45.488414 145.996134 1.000000
lik[0,100]=584.313279
lik[100,200]=577.951462
lik[200,300]=550.653673
lik[300,400]=534.702716
lik[400,500]=545.289629
lik[500,600]=552.679972
lik[600,700]=553.115422
lik[700,800]=548.856534
lik[800,900]=551.621203
lik[900,1000]=579.631421
total lik[0,1000]: 5578.815310
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
35.025230 43.448001 145.399257 1.000000
lik[0,100]=580.928737
lik[100,200]=574.506993
lik[200,300]=545.857931
lik[300,400]=529.515869
lik[400,500]=540.602018
lik[500,600]=548.107828
lik[600,700]=551.539982
lik[700,800]=545.950003
lik[800,900]=548.132827
lik[900,1000]=574.840401
total lik[0,1000]: 5539.982589
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
33.678752 45.706794 144.957542 1.000000
lik[0,100]=580.624164
lik[100,200]=574.366474
lik[200,300]=544.794589
lik[300,400]=528.846178
lik[400,500]=539.295123
lik[500,600]=547.365455
lik[600,700]=550.906986
lik[700,800]=544.351509
lik[800,900]=547.248654
lik[900,1000]=574.564962
total lik[0,1000]: 5532.364094
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
33.824088 45.478856 145.002324 1.000000
lik[0,100]=580.586342
lik[100,200]=574.319487
lik[200,300]=544.817785
lik[300,400]=528.812196
lik[400,500]=539.305333
lik[500,600]=547.353145
lik[600,700]=550.894066
lik[700,800]=544.403259
lik[800,900]=547.256750
lik[900,1000]=574.516260
total lik[0,1000]: 5532.264622
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
33.818569 45.464950 145.002550 1.000000
lik[0,100]=580.584641
lik[100,200]=574.316384
lik[200,300]=544.815909
lik[300,400]=528.809922
lik[400,500]=539.307849
lik[500,600]=547.351457
lik[600,700]=550.899268
lik[700,800]=544.409829
lik[800,900]=547.257485
lik[900,1000]=574.511741
total lik[0,1000]: 5532.264486
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
33.817497 45.459067 145.002427 1.000000
lik[0,100]=580.583984
lik[100,200]=574.315126
lik[200,300]=544.814834
lik[300,400]=528.809033
lik[400,500]=539.308812
lik[500,600]=547.350873
lik[600,700]=550.901602
lik[700,800]=544.412381
lik[800,900]=547.257816
lik[900,1000]=574.510007
total lik[0,1000]: 5532.264467
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
33.819222 45.456457 145.002373 1.000000
lik[0,100]=580.583734
lik[100,200]=574.314663
lik[200,300]=544.814406
lik[300,400]=528.808768
lik[400,500]=539.309065
lik[500,600]=547.350841
lik[600,700]=550.902327
lik[700,800]=544.413105
lik[800,900]=547.258002
lik[900,1000]=574.509549
total lik[0,1000]: 5532.264459
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
33.832761 45.444764 145.002204 1.000000
lik[0,100]=580.582715
lik[100,200]=574.312838
lik[200,300]=544.812712
lik[300,400]=528.807921
lik[400,500]=539.309743
lik[500,600]=547.351305
lik[600,700]=550.904662
lik[700,800]=544.415272
lik[800,900]=547.258938
lik[900,1000]=574.508318
total lik[0,1000]: 5532.264422
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
33.864406 45.424697 145.002024 1.000000
lik[0,100]=580.581108
lik[100,200]=574.310068
lik[200,300]=544.810139
lik[300,400]=528.806965
lik[400,500]=539.310243
lik[500,600]=547.352976
lik[600,700]=550.907336
lik[700,800]=544.417428
lik[800,900]=547.260697
lik[900,1000]=574.507397
total lik[0,1000]: 5532.264358
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
33.938938 45.385626 145.001843 1.000000
lik[0,100]=580.578196
lik[100,200]=574.305228
lik[200,300]=544.805645
lik[300,400]=528.805865
lik[400,500]=539.310196
lik[500,600]=547.357587
lik[600,700]=550.910490
lik[700,800]=544.419224
lik[800,900]=547.264362
lik[900,1000]=574.507441
total lik[0,1000]: 5532.264234
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
34.037751 45.343100 145.001987 1.000000
lik[0,100]=580.575307
lik[100,200]=574.300721
lik[200,300]=544.801609
lik[300,400]=528.805721
lik[400,500]=539.308741
lik[500,600]=547.364475
lik[600,700]=550.910951
lik[700,800]=544.417868
lik[800,900]=547.268682
lik[900,1000]=574.510020
total lik[0,1000]: 5532.264095
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
34.085437 45.329496 145.002296 1.000000
lik[0,100]=580.574649
lik[100,200]=574.299977
lik[200,300]=544.801038
lik[300,400]=528.806630
lik[400,500]=539.307001
lik[500,600]=547.368363
lik[600,700]=550.908460
lik[700,800]=544.414427
lik[800,900]=547.270356
lik[900,1000]=574.513139
total lik[0,1000]: 5532.264040
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
34.083537 45.334389 145.002242 1.000000
lik[0,100]=580.575168
lik[100,200]=574.300904
lik[200,300]=544.801652
lik[300,400]=528.807202
lik[400,500]=539.306414
lik[500,600]=547.368551
lik[600,700]=550.907123
lik[700,800]=544.412817
lik[800,900]=547.270022
lik[900,1000]=574.514183
total lik[0,1000]: 5532.264035
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
34.080148 45.336411 145.002245 1.000000
lik[0,100]=580.575328
lik[100,200]=574.301175
lik[200,300]=544.801887
lik[300,400]=528.807285
lik[400,500]=539.306379
lik[500,600]=547.368358
lik[600,700]=550.906902
lik[700,800]=544.412638
lik[800,900]=547.269838
lik[900,1000]=574.514245
total lik[0,1000]: 5532.264034
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: 34.080148 (28.567784,39.592511), sigma_anc: 45.336411 (42.680682,47.992139), mu_mod: 145.002245 (144.936825,145.067665), sigma_mod: 1.000000 (-nan,-nan), nfunctioncalls: 377 ngradientcalls: 373, llh: -5532.264034.
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