Stutter model failed to converge at a site #46

nh13 · 2017-11-08T16:38:47Z

I have in interesting case where the stutter model fails to converge. My goal is to force STR to genotype these sites, as I have a few false-negatives that have great coverage.

After increasing the values for ABS_LL_CONVERGE and FRAC_LL_CONVERGE in genotyper_bam_processor, it correctly genotypes the locus.

Would these be candidates for command line options or a configuration file?

Here's the log output after changing `false` to `true` to enable logging on this line: https://github.com/tfwillems/HipSTR/blob/master/src/genotyper_bam_processor.cpp#L143 (I also added an extra log message).

HipSTR --bams in.bam --fasta ref.fasta --regions regions.bed \
              --str-vcf out.vcf.gz \
              --output-gls \
              --output-pls \
              --output-filters \
              --min-reads 1 \
              --use-unpaired \
              --no-rmdup \
              --haploid-chrs 21 \
              --max-str-len 150 \
              --max-hap-flanks 10 \
              --min-flank-freq 0.1
Detected 1 BAM/CRAM files
BAMs/CRAMs contain unique read group IDs for 2042 unique libraries and 2042 unique samples
Reading region file CORIELL_16/tmp/genotype/PentaD.regions.bed
Region file contains 1 regions

Processing region 21 45056084 45056150
39995 reads overlapped region, of which 
	0 were hard clipped
	3 had an 'N' base call
	17754 had low base quality scores
	14 did not have a unique mapping
	22224 PASSED ALL FILTERS
Found 20530 fully paired reads and 1694 unpaired reads for downstream analyses
Phased SNPs add info for 0 out of 22224 reads and 0 out of 386 samples
Building EM stutter model
Training EM stutter model
Iteration 1: LL = -7191.35

	IN_FRAME [P_GEOM(rep)=0.9, P_DOWN=0.1, P_UP=0.1]
	OUT_FRAME[P_GEOM(bp) =0.8, P_DOWN=0.01, P_UP=0.01]
Pop freqs: 0.0400246 0.0401176 0.0400392 0.0434675 0.0400168 0.0400134 0.0409605 0.15168 0.0413104 0.0400134 0.0404268 0.0400907 0.0400056 0.040028 0.0410131 0.0400616 0.0400134 0.0405977 0.0400593 0.040028 0.040019 0.0400134 
1.79769e+308 0.01 1 0.001
Iteration 2: LL = -4119.45

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0397135 0.0398058 0.039728 0.0431297 0.0397058 0.0397024 0.0406422 0.158273 0.0409894 0.0397024 0.0401126 0.0397791 0.0396947 0.0397169 0.0406944 0.0397503 0.0397024 0.0402821 0.039748 0.0397169 0.039708 0.0397024 
3071.9 0.01 0.427166 0.001
Iteration 3: LL = -4119.33

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0394049 0.0394964 0.0394192 0.0427945 0.0393972 0.0393939 0.0403263 0.164815 0.0406708 0.0393939 0.0398008 0.0394699 0.0393862 0.0394082 0.0403781 0.0394413 0.0393939 0.0399691 0.039439 0.0394082 0.0393994 0.0393939 
0.121505 0.01 2.94955e-05 0.001
Iteration 4: LL = -4119.22

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0390986 0.0391894 0.0391129 0.0424619 0.039091 0.0390877 0.0400129 0.171306 0.0403547 0.0390877 0.0394915 0.0391631 0.03908 0.039102 0.0400643 0.0391348 0.0390877 0.0396584 0.0391325 0.039102 0.0390932 0.0390877 
0.115885 0.01 2.81319e-05 0.001
Iteration 5: LL = -4119.11

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0387948 0.0388849 0.0388089 0.0421319 0.0387872 0.0387839 0.0397019 0.177747 0.0400411 0.0387839 0.0391846 0.0388588 0.0387763 0.038798 0.0397529 0.0388306 0.0387839 0.0393502 0.0388284 0.038798 0.0387893 0.0387839 
0.110723 0.01 2.68796e-05 0.001
Iteration 6: LL = -4119

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0384932 0.0385827 0.0385073 0.0418044 0.0384857 0.0384825 0.0393934 0.184137 0.0397299 0.0384825 0.03888 0.0385568 0.0384749 0.0384965 0.0394439 0.0385288 0.0384825 0.0390444 0.0385266 0.0384965 0.0384879 0.0384825 
0.105966 0.01 2.57255e-05 0.001
Iteration 7: LL = -4118.9

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0381941 0.0382828 0.038208 0.0414795 0.0381866 0.0381834 0.0390872 0.190478 0.0394211 0.0381834 0.0385779 0.0382571 0.0381759 0.0381973 0.0391374 0.0382294 0.0381834 0.0387409 0.0382272 0.0381973 0.0381887 0.0381834 
0.101568 0.01 2.46585e-05 0.001
Iteration 8: LL = -4118.8

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0378972 0.0379853 0.037911 0.0411571 0.0378898 0.0378866 0.0387834 0.19677 0.0391147 0.0378866 0.038278 0.0379598 0.0378792 0.0379004 0.0388332 0.0379323 0.0378866 0.0384398 0.0379301 0.0379004 0.0378919 0.0378866 
0.0974907 0.01 2.36691e-05 0.001
Iteration 9: LL = -4118.71

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0376027 0.03769 0.0376164 0.0408373 0.0375953 0.0375922 0.038482 0.203012 0.0388107 0.0375922 0.0379805 0.0376647 0.0375848 0.0376059 0.0385314 0.0376375 0.0375922 0.0381411 0.0376353 0.0376059 0.0375974 0.0375922 
0.0936995 0.01 2.27492e-05 0.001
Iteration 10: LL = -4118.62

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0373104 0.0373971 0.037324 0.0405199 0.0373031 0.0373 0.0381829 0.209207 0.0385091 0.0373 0.0376853 0.037372 0.0372927 0.0373136 0.0382319 0.0373449 0.0373 0.0378446 0.0373428 0.0373136 0.0373052 0.0373 
0.0901657 0.01 2.18917e-05 0.001
Iteration 11: LL = -4118.53

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0370205 0.0371065 0.0370339 0.0402049 0.0370132 0.0370101 0.0378861 0.215353 0.0382098 0.0370101 0.0373925 0.0370816 0.0370029 0.0370236 0.0379348 0.0370547 0.0370101 0.0375505 0.0370525 0.0370236 0.0370153 0.0370101 
0.0868641 0.01 2.10906e-05 0.001
Iteration 12: LL = -4118.45

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0367327 0.0368181 0.0367461 0.0398925 0.0367255 0.0367225 0.0375917 0.221451 0.0379128 0.0367225 0.0371018 0.0367934 0.0367153 0.0367359 0.03764 0.0367667 0.0367225 0.0372587 0.0367646 0.0367359 0.0367276 0.0367225 
0.0837725 0.01 2.03404e-05 0.001
Iteration 13: LL = -4118.37

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0364472 0.0365319 0.0364605 0.0395824 0.0364401 0.0364371 0.0372995 0.227502 0.0376181 0.0364371 0.0368135 0.0365074 0.0364299 0.0364503 0.0373474 0.0364809 0.0364371 0.0369691 0.0364788 0.0364503 0.0364422 0.0364371 
0.0808717 0.01 1.96365e-05 0.001
Iteration 14: LL = -4118.29

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.036164 0.036248 0.0361772 0.0392748 0.0361569 0.0361539 0.0370096 0.233506 0.0373258 0.0361539 0.0365274 0.0362237 0.0361468 0.0361671 0.0370572 0.0361974 0.0361539 0.0366818 0.0361953 0.0361671 0.0361589 0.0361539 
0.0781446 0.01 1.89747e-05 0.001
Iteration 15: LL = -4118.21

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0358829 0.0359663 0.035896 0.0389695 0.0358759 0.0358729 0.036722 0.239463 0.0370357 0.0358729 0.0362435 0.0359421 0.0358659 0.035886 0.0367691 0.0359161 0.0358729 0.0363967 0.035914 0.035886 0.0358779 0.0358729 
0.0755761 0.01 1.83513e-05 0.001
Iteration 16: LL = -4118.14

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.035604 0.0356867 0.035617 0.0386667 0.0355971 0.0355941 0.0364366 0.245374 0.0367478 0.0355941 0.0359618 0.0356628 0.0355871 0.0356071 0.0364834 0.0356369 0.0355941 0.0361138 0.0356349 0.0356071 0.0355991 0.0355941 
0.0731529 0.01 1.77633e-05 0.001
Iteration 17: LL = -4118.07

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0353273 0.0354094 0.0353402 0.0383662 0.0353204 0.0353174 0.0361534 0.251239 0.0364622 0.0353174 0.0356823 0.0353856 0.0353105 0.0353303 0.0361998 0.03536 0.0353174 0.0358331 0.0353579 0.0353303 0.0353224 0.0353174 
0.070863 0.01 1.72075e-05 0.001
Iteration 18: LL = -4118

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0350527 0.0351342 0.0350655 0.038068 0.0350459 0.035043 0.0358724 0.257058 0.0361788 0.035043 0.035405 0.0351106 0.0350361 0.0350557 0.0359185 0.0350852 0.035043 0.0355546 0.0350831 0.0350557 0.0350479 0.035043 
0.0686957 0.01 1.66815e-05 0.001
Iteration 19: LL = -4117.93

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0347803 0.0348611 0.034793 0.0377721 0.0347735 0.0347706 0.0355936 0.262832 0.0358977 0.0347706 0.0351298 0.0348377 0.0347638 0.0347833 0.0356393 0.0348125 0.0347706 0.0352783 0.0348105 0.0347833 0.0347755 0.0347706 
0.0666417 0.01 1.6183e-05 0.001
Iteration 20: LL = -4117.87

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.03451 0.0345902 0.0345226 0.0374785 0.0345032 0.0345004 0.035317 0.268562 0.0356187 0.0345004 0.0348568 0.034567 0.0344936 0.0345129 0.0353623 0.0345419 0.0345004 0.0350041 0.0345399 0.0345129 0.0345052 0.0345004 
0.0646921 0.01 1.57099e-05 0.001
Iteration 21: LL = -4117.8

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0342418 0.0343213 0.0342543 0.0371873 0.0342351 0.0342322 0.0350425 0.274246 0.0353418 0.0342322 0.0345859 0.0342983 0.0342255 0.0342447 0.0350875 0.0342735 0.0342322 0.034732 0.0342715 0.0342447 0.034237 0.0342322 
0.0628395 0.01 1.52602e-05 0.001
Iteration 22: LL = -4117.74

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0339757 0.0340546 0.033988 0.0368982 0.033969 0.0339662 0.0347701 0.279887 0.0350672 0.0339662 0.0343171 0.0340317 0.0339595 0.0339786 0.0348148 0.0340071 0.0339662 0.0344621 0.0340051 0.0339786 0.0339709 0.0339662 
0.0610766 0.01 1.48323e-05 0.001
Iteration 23: LL = -4117.68

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0337116 0.0337899 0.0337239 0.0366115 0.033705 0.0337022 0.0344999 0.285484 0.0347946 0.0337022 0.0340504 0.0337672 0.0336956 0.0337145 0.0345442 0.0337428 0.0337022 0.0341943 0.0337408 0.0337145 0.0337069 0.0337022 
0.0593973 0.01 1.44247e-05 0.001
Iteration 24: LL = -4117.63

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0334496 0.0335273 0.0334618 0.0363269 0.033443 0.0334403 0.0342318 0.291037 0.0345242 0.0334403 0.0337857 0.0335048 0.0334337 0.0334524 0.0342757 0.0334805 0.0334403 0.0339285 0.0334786 0.0334524 0.0334449 0.0334403 
0.0577957 0.01 1.4036e-05 0.001
Iteration 25: LL = -4117.57

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0331896 0.0332667 0.0332017 0.0360446 0.0331831 0.0331804 0.0339657 0.296547 0.0342559 0.0331804 0.0335231 0.0332444 0.0331739 0.0331924 0.0340093 0.0332203 0.0331804 0.0336648 0.0332184 0.0331924 0.033185 0.0331804 
0.0562667 0.01 1.36648e-05 0.001
Iteration 26: LL = -4117.52

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0329317 0.0330082 0.0329437 0.0357644 0.0329252 0.0329225 0.0337017 0.302014 0.0339896 0.0329225 0.0332626 0.032986 0.032916 0.0329345 0.033745 0.0329621 0.0329225 0.0334032 0.0329602 0.0329345 0.0329271 0.0329225 
0.0548054 0.01 1.33101e-05 0.001
Iteration 27: LL = -4117.46

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0326757 0.0327516 0.0326876 0.0354865 0.0326693 0.0326666 0.0334398 0.307439 0.0337255 0.0326666 0.0330041 0.0327297 0.0326602 0.0326785 0.0334828 0.0327059 0.0326666 0.0331436 0.0327041 0.0326785 0.0326712 0.0326666 
0.0534076 0.01 1.29708e-05 0.001
Iteration 28: LL = -4117.41

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0324218 0.0324971 0.0324336 0.0352107 0.0324154 0.0324127 0.0331799 0.312822 0.0334634 0.0324127 0.0327476 0.0324753 0.0324064 0.0324245 0.0332225 0.0324517 0.0324127 0.032886 0.0324499 0.0324245 0.0324172 0.0324127 
0.0520691 0.01 1.26459e-05 0.001
Iteration 29: LL = -4117.36

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0321698 0.0322445 0.0321815 0.034937 0.0321635 0.0321608 0.032922 0.318162 0.0332033 0.0321608 0.032493 0.0322229 0.0321545 0.0321725 0.0329643 0.0321995 0.0321608 0.0326304 0.0321977 0.0321725 0.0321653 0.0321608 
0.0507863 0.01 1.23345e-05 0.001
Iteration 30: LL = -4117.31

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0319198 0.0319939 0.0319314 0.0346655 0.0319135 0.0319108 0.0326662 0.323462 0.0329452 0.0319108 0.0322405 0.0319724 0.0319046 0.0319225 0.0327081 0.0319493 0.0319108 0.0323768 0.0319474 0.0319225 0.0319153 0.0319108 
0.0495559 0.01 1.20358e-05 0.001
Iteration 31: LL = -4117.26

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0316717 0.0317453 0.0316832 0.0343961 0.0316655 0.0316628 0.0324123 0.32872 0.0326892 0.0316628 0.0319899 0.031724 0.0316566 0.0316744 0.0324539 0.031701 0.0316628 0.0321251 0.0316991 0.0316744 0.0316673 0.0316628 
0.0483747 0.01 1.17491e-05 0.001
Iteration 32: LL = -4117.21

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0314255 0.0314985 0.031437 0.0341287 0.0314194 0.0314168 0.0321604 0.333937 0.0324351 0.0314168 0.0317413 0.0314774 0.0314106 0.0314282 0.0322017 0.0314546 0.0314168 0.0318755 0.0314528 0.0314282 0.0314211 0.0314168 
0.0472399 0.01 1.14736e-05 0.001
Iteration 33: LL = -4117.17

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0311813 0.0312537 0.0311927 0.0338635 0.0311752 0.0311726 0.0319104 0.339114 0.032183 0.0311726 0.0314946 0.0312327 0.0311665 0.0311839 0.0319514 0.0312101 0.0311726 0.0316277 0.0312083 0.0311839 0.0311769 0.0311726 
0.0461489 0.01 1.12088e-05 0.001
Iteration 34: LL = -4117.12

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.030939 0.0310108 0.0309502 0.0336003 0.0309329 0.0309303 0.0316624 0.34425 0.0319329 0.0309303 0.0312498 0.03099 0.0309243 0.0309416 0.0317031 0.0309676 0.0309303 0.0313819 0.0309658 0.0309416 0.0309346 0.0309303 
0.0450991 0.01 1.09539e-05 0.001
Iteration 35: LL = -4117.08

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0306985 0.0307698 0.0307097 0.0333392 0.0306925 0.0306899 0.0314163 0.349347 0.0316847 0.0306899 0.031007 0.0307492 0.0306839 0.0307011 0.0314567 0.0307269 0.0306899 0.031138 0.0307251 0.0307011 0.0306942 0.0306899 
0.0440884 0.01 1.07085e-05 0.001
Iteration 36: LL = -4117.04

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0304599 0.0305307 0.030471 0.0330801 0.0304539 0.0304514 0.0311722 0.354403 0.0314385 0.0304514 0.030766 0.0305102 0.0304454 0.0304625 0.0312122 0.0304881 0.0304514 0.030896 0.0304863 0.0304625 0.0304556 0.0304514 
0.0431146 0.01 1.04721e-05 0.001
Iteration 37: LL = -4116.99

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0302232 0.0302934 0.0302342 0.032823 0.0302173 0.0302147 0.0309299 0.359421 0.0311941 0.0302147 0.0305269 0.030273 0.0302088 0.0302257 0.0309696 0.0302511 0.0302147 0.0306559 0.0302494 0.0302257 0.0302189 0.0302147 
0.0421757 0.01 1.02442e-05 0.001
Iteration 38: LL = -4116.95

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0299883 0.0300579 0.0299992 0.0325679 0.0299824 0.0299799 0.0306895 0.3644 0.0309517 0.0299799 0.0302896 0.0300378 0.029974 0.0299908 0.0307289 0.030016 0.0299799 0.0304176 0.0300143 0.0299908 0.0299841 0.0299799 
0.0412699 0.01 1.00243e-05 0.001
Iteration 39: LL = -4116.91

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0297552 0.0298243 0.029766 0.0323147 0.0297494 0.0297469 0.030451 0.36934 0.0307111 0.0297469 0.0300542 0.0298043 0.0297411 0.0297577 0.0304901 0.0297827 0.0297469 0.0301812 0.029781 0.0297577 0.029751 0.0297469 
0.0403956 0.01 9.81202e-06 0.001
Iteration 40: LL = -4116.87

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0295239 0.0295925 0.0295347 0.0320636 0.0295182 0.0295157 0.0302143 0.374241 0.0304724 0.0295157 0.0298206 0.0295727 0.0295099 0.0295265 0.0302531 0.0295512 0.0295157 0.0299467 0.0295495 0.0295265 0.0295198 0.0295157 
0.0395511 0.01 9.60699e-06 0.001
Iteration 41: LL = -4116.83

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0292945 0.0293625 0.0293052 0.0318144 0.0292888 0.0292863 0.0299795 0.379104 0.0302356 0.0292863 0.0295888 0.0293428 0.0292806 0.029297 0.030018 0.0293216 0.0292863 0.0297139 0.0293199 0.029297 0.0292904 0.0292863 
0.0387351 0.01 9.40885e-06 0.001
Iteration 42: LL = -4116.8

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0290668 0.0291343 0.0290774 0.0315671 0.0290611 0.0290587 0.0297465 0.38393 0.0300006 0.0290587 0.0293589 0.0291148 0.029053 0.0290693 0.0297847 0.0290937 0.0290587 0.029483 0.029092 0.0290693 0.0290627 0.0290587 
0.0379459 0.01 9.21727e-06 0.001
Iteration 43: LL = -4116.76

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0288409 0.0289079 0.0288514 0.0313218 0.0288353 0.0288328 0.0295153 0.388718 0.0297674 0.0288328 0.0291307 0.0288885 0.0288272 0.0288434 0.0295532 0.0288676 0.0288328 0.0292538 0.0288659 0.0288434 0.0288369 0.0288328 
0.0371825 0.01 9.03191e-06 0.001
Iteration 44: LL = -4116.72

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0286167 0.0286832 0.0286272 0.0310783 0.0286111 0.0286088 0.0292859 0.393469 0.0295361 0.0286088 0.0289043 0.028664 0.0286032 0.0286192 0.0293235 0.0286432 0.0286088 0.0290265 0.0286416 0.0286192 0.0286128 0.0286088 
0.0364436 0.01 8.8525e-06 0.001
Iteration 45: LL = -4116.69

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0283943 0.0284603 0.0284047 0.0308368 0.0283888 0.0283864 0.0290583 0.398183 0.0293065 0.0283864 0.0286797 0.0284412 0.0283808 0.0283968 0.0290956 0.0284206 0.0283864 0.0288009 0.0284189 0.0283968 0.0283904 0.0283864 
0.035728 0.01 8.67875e-06 0.001
Iteration 46: LL = -4116.65

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0281737 0.0282391 0.0281839 0.0305971 0.0281681 0.0281658 0.0288325 0.40286 0.0290788 0.0281658 0.0284568 0.0282201 0.0281603 0.0281761 0.0288695 0.0281997 0.0281658 0.028577 0.0281981 0.0281761 0.0281697 0.0281658 
0.0350347 0.01 8.51042e-06 0.001
Iteration 47: LL = -4116.62

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0279547 0.0280196 0.0279649 0.0303593 0.0279492 0.0279469 0.0286084 0.407501 0.0288528 0.0279469 0.0282356 0.0280008 0.0279414 0.0279571 0.0286451 0.0279805 0.0279469 0.0283549 0.0279789 0.0279571 0.0279508 0.0279469 
0.0343627 0.01 8.34724e-06 0.001
Iteration 48: LL = -4116.58

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0277374 0.0278019 0.0277475 0.0301234 0.027732 0.0277297 0.028386 0.412106 0.0286285 0.0277297 0.0280161 0.0277832 0.0277242 0.0277398 0.0284225 0.0277631 0.0277297 0.0281346 0.0277615 0.0277398 0.0277336 0.0277297 
0.033711 0.01 8.189e-06 0.001
Iteration 49: LL = -4116.55

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0275219 0.0275858 0.0275319 0.0298893 0.0275165 0.0275142 0.0281654 0.416675 0.028406 0.0275142 0.0277984 0.0275673 0.0275088 0.0275242 0.0282016 0.0275473 0.0275142 0.0279159 0.0275457 0.0275242 0.027518 0.0275142 
0.0330787 0.01 8.03547e-06 0.001
Iteration 50: LL = -4116.52

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.027308 0.0273714 0.0273179 0.029657 0.0273026 0.0273003 0.0279465 0.421209 0.0281852 0.0273003 0.0275824 0.027353 0.027295 0.0273103 0.0279824 0.0273332 0.0273003 0.0276989 0.0273316 0.0273103 0.0273041 0.0273003 
0.032465 0.01 7.88646e-06 0.001
Iteration 51: LL = -4116.49

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0270957 0.0271587 0.0271056 0.0294265 0.0270904 0.0270881 0.0277293 0.425707 0.0279662 0.0270881 0.027368 0.0271404 0.0270828 0.027098 0.0277649 0.0271208 0.0270881 0.0274837 0.0271192 0.027098 0.0270919 0.0270881 
0.0318692 0.01 7.74178e-06 0.001
Iteration 52: LL = -4116.45

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0268851 0.0269476 0.0268949 0.0291978 0.0268799 0.0268776 0.0275138 0.430171 0.0277488 0.0268776 0.0271553 0.0269295 0.0268723 0.0268874 0.0275491 0.02691 0.0268776 0.02727 0.0269084 0.0268874 0.0268814 0.0268776 
0.0312904 0.01 7.60123e-06 0.001
Iteration 53: LL = -4116.42

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0266762 0.0267381 0.0266859 0.0289708 0.0266709 0.0266687 0.0273 0.4346 0.0275332 0.0266687 0.0269442 0.0267202 0.0266635 0.0266784 0.027335 0.0267008 0.0266687 0.0270581 0.0266993 0.0266784 0.0266724 0.0266687 
0.0307279 0.01 7.46465e-06 0.001
Iteration 54: LL = -4116.39

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0264688 0.0265303 0.0264785 0.0287457 0.0264637 0.0264614 0.0270878 0.438994 0.0273192 0.0264614 0.0267348 0.0265125 0.0264563 0.0264711 0.0271226 0.0264933 0.0264614 0.0268478 0.0264918 0.0264711 0.0264651 0.0264614 
0.0301811 0.01 7.33189e-06 0.001
Iteration 55: LL = -4116.36

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0262631 0.0263241 0.0262727 0.0285223 0.026258 0.0262558 0.0268773 0.443354 0.0271069 0.0262558 0.026527 0.0263065 0.0262506 0.0262654 0.0269118 0.0262874 0.0262558 0.0266391 0.0262859 0.0262654 0.0262595 0.0262558 
0.0296494 0.01 7.20277e-06 0.001
Iteration 56: LL = -4116.33

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.026059 0.0261195 0.0260685 0.0283006 0.0260539 0.0260517 0.0266684 0.44768 0.0268962 0.0260517 0.0263209 0.026102 0.0260466 0.0260612 0.0267026 0.0260831 0.0260517 0.0264321 0.0260816 0.0260612 0.0260554 0.0260517 
0.0291322 0.01 7.07717e-06 0.001
Iteration 57: LL = -4116.31

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0258565 0.0259165 0.0258659 0.0280806 0.0258514 0.0258493 0.0264611 0.451973 0.0266871 0.0258493 0.0261163 0.0258991 0.0258442 0.0258587 0.0264951 0.0258804 0.0258493 0.0262267 0.0258789 0.0258587 0.0258529 0.0258493 
0.0286289 0.01 6.95494e-06 0.001
Iteration 58: LL = -4116.28

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0256555 0.0257151 0.0256649 0.0278624 0.0256505 0.0256484 0.0262554 0.456232 0.0264797 0.0256484 0.0259133 0.0256979 0.0256433 0.0256577 0.0262892 0.0256792 0.0256484 0.0260228 0.0256778 0.0256577 0.0256519 0.0256484 
0.0281389 0.01 6.83595e-06 0.001
Iteration 59: LL = -4116.25

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0254561 0.0255153 0.0254654 0.0276459 0.0254511 0.025449 0.0260514 0.460458 0.0262739 0.025449 0.0257119 0.0254981 0.025444 0.0254583 0.0260848 0.0254797 0.025449 0.0258206 0.0254782 0.0254583 0.0254526 0.025449 
0.0276617 0.01 6.72008e-06 0.001
Iteration 60: LL = -4116.22

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0252583 0.025317 0.0252675 0.027431 0.0252533 0.0252512 0.0258489 0.464652 0.0260697 0.0252512 0.0255121 0.0253 0.0252463 0.0252604 0.0258821 0.0252816 0.0252512 0.0256199 0.0252802 0.0252604 0.0252548 0.0252512 
0.0271969 0.01 6.60721e-06 0.001
Iteration 61: LL = -4116.2

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.025062 0.0251202 0.0250711 0.0272178 0.0250571 0.025055 0.025648 0.468812 0.0258671 0.025055 0.0253138 0.0251033 0.0250501 0.0250641 0.025681 0.0250851 0.025055 0.0254208 0.0250837 0.0250641 0.0250585 0.025055 
0.026744 0.01 6.49723e-06 0.001
Iteration 62: LL = -4116.17

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0248672 0.024925 0.0248763 0.0270063 0.0248623 0.0248602 0.0254487 0.472941 0.0256661 0.0248602 0.0251171 0.0249082 0.0248554 0.0248693 0.0254814 0.0248902 0.0248602 0.0252232 0.0248887 0.0248693 0.0248637 0.0248602 
0.0263026 0.01 6.39003e-06 0.001
Iteration 63: LL = -4116.14

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0246739 0.0247312 0.0246829 0.0267964 0.0246691 0.024667 0.0252509 0.477037 0.0254666 0.024667 0.0249219 0.0247146 0.0246622 0.024676 0.0252833 0.0246967 0.024667 0.0250272 0.0246953 0.024676 0.0246705 0.024667 
0.0258722 0.01 6.28551e-06 0.001
Iteration 64: LL = -4116.12

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0244822 0.024539 0.0244911 0.0265881 0.0244774 0.0244753 0.0250546 0.481102 0.0252687 0.0244753 0.0247282 0.0245226 0.0244705 0.0244842 0.0250868 0.0245048 0.0244753 0.0248327 0.0245034 0.0244842 0.0244787 0.0244753 
0.0254525 0.01 6.18358e-06 0.001
Iteration 65: LL = -4116.09

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0242919 0.0243483 0.0243007 0.0263815 0.0242871 0.0242851 0.0248599 0.485134 0.0250723 0.0242851 0.024536 0.024332 0.0242803 0.0242939 0.0248918 0.0243143 0.0242851 0.0246397 0.0243129 0.0242939 0.0242885 0.0242851 
0.025043 0.01 6.08414e-06 0.001
Iteration 66: LL = -4116.07

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0241031 0.0241591 0.0241119 0.0261764 0.0240984 0.0240963 0.0246667 0.489136 0.0248774 0.0240963 0.0243453 0.0241429 0.0240916 0.0241051 0.0246984 0.0241254 0.0240963 0.0244482 0.024124 0.0241051 0.0240997 0.0240963 
0.0246435 0.01 5.9871e-06 0.001
Iteration 67: LL = -4116.04

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0239158 0.0239713 0.0239245 0.025973 0.0239111 0.0239091 0.024475 0.493106 0.0246841 0.0239091 0.0241561 0.0239552 0.0239044 0.0239178 0.0245064 0.0239379 0.0239091 0.0242582 0.0239365 0.0239178 0.0239124 0.0239091 
0.0242535 0.01 5.89239e-06 0.001
Iteration 68: LL = -4116.02

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0237299 0.023785 0.0237385 0.0257711 0.0237252 0.0237233 0.0242848 0.497046 0.0244922 0.0237233 0.0239683 0.023769 0.0237186 0.0237319 0.024316 0.0237518 0.0237233 0.0240696 0.0237504 0.0237319 0.0237266 0.0237233 
0.0238727 0.01 5.79992e-06 0.001
Iteration 69: LL = -4116

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0235455 0.0236001 0.023554 0.0255708 0.0235408 0.0235389 0.024096 0.500955 0.0243019 0.0235389 0.023782 0.0235843 0.0235343 0.0235475 0.024127 0.0235672 0.0235389 0.0238826 0.0235659 0.0235475 0.0235422 0.0235389 
0.0235009 0.01 5.70962e-06 0.001
Iteration 70: LL = -4115.97

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0233625 0.0234167 0.023371 0.0253721 0.0233579 0.0233559 0.0239088 0.504834 0.024113 0.0233559 0.0235972 0.023401 0.0233514 0.0233644 0.0239395 0.0233841 0.0233559 0.0236969 0.0233827 0.0233644 0.0233592 0.0233559 
0.0231377 0.01 5.62141e-06 0.001
Iteration 71: LL = -4115.95

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0231809 0.0232347 0.0231893 0.0251749 0.0231763 0.0231744 0.0237229 0.508682 0.0239256 0.0231744 0.0234138 0.0232191 0.0231699 0.0231829 0.0237534 0.0232023 0.0231744 0.0235128 0.023201 0.0231829 0.0231776 0.0231744 
0.0227828 0.01 5.53523e-06 0.001
Iteration 72: LL = -4115.93

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0230007 0.0230541 0.0230091 0.0249792 0.0229962 0.0229943 0.0235386 0.512501 0.0237396 0.0229943 0.0232318 0.0230387 0.0229898 0.0230027 0.0235688 0.023022 0.0229943 0.02333 0.0230207 0.0230027 0.0229975 0.0229943 
0.0224361 0.01 5.451e-06 0.001
Iteration 73: LL = -4115.91

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.022822 0.022875 0.0228303 0.0247851 0.0228175 0.0228156 0.0233556 0.516289 0.0235551 0.0228156 0.0230513 0.0228596 0.0228111 0.0228239 0.0233856 0.0228431 0.0228156 0.0231487 0.0228417 0.0228239 0.0228188 0.0228156 
0.0220971 0.01 5.36867e-06 0.001
Iteration 74: LL = -4115.89

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0226446 0.0226972 0.0226528 0.0245925 0.0226402 0.0226383 0.0231741 0.520049 0.0233721 0.0226383 0.0228721 0.022682 0.0226338 0.0226465 0.0232039 0.0226655 0.0226383 0.0229688 0.0226642 0.0226465 0.0226414 0.0226383 
0.0217656 0.01 5.28817e-06 0.001
Iteration 75: LL = -4115.86

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0224686 0.0225208 0.0224768 0.0244013 0.0224642 0.0224623 0.022994 0.523779 0.0231904 0.0224623 0.0226944 0.0225057 0.0224579 0.0224705 0.0230235 0.0224894 0.0224623 0.0227903 0.0224881 0.0224705 0.0224655 0.0224623 
0.0214415 0.01 5.20945e-06 0.001
Iteration 76: LL = -4115.84

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.022294 0.0223458 0.0223021 0.0242117 0.0222896 0.0222877 0.0228153 0.52748 0.0230102 0.0222877 0.022518 0.0223308 0.0222834 0.0222959 0.0228446 0.0223146 0.0222877 0.0226132 0.0223133 0.0222959 0.0222909 0.0222877 
0.0211245 0.01 5.13245e-06 0.001
Iteration 77: LL = -4115.82

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0221207 0.0221721 0.0221288 0.0240235 0.0221164 0.0221145 0.022638 0.531153 0.0228313 0.0221145 0.022343 0.0221572 0.0221102 0.0221226 0.022667 0.0221411 0.0221145 0.0224374 0.0221399 0.0221226 0.0221176 0.0221145 
0.0208143 0.01 5.05711e-06 0.001
Iteration 78: LL = -4115.8

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0219488 0.0219998 0.0219568 0.0238368 0.0219445 0.0219426 0.022462 0.534797 0.0226539 0.0219426 0.0221693 0.021985 0.0219383 0.0219506 0.0224909 0.0219691 0.0219426 0.022263 0.0219678 0.0219506 0.0219457 0.0219426 
0.0205108 0.01 4.98339e-06 0.001
Iteration 79: LL = -4115.78

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0217782 0.0218288 0.0217861 0.0236515 0.0217739 0.0217721 0.0222874 0.538412 0.0224778 0.0217721 0.021997 0.0218141 0.0217678 0.02178 0.0223161 0.0217983 0.0217721 0.02209 0.0217971 0.02178 0.0217751 0.0217721 
0.0202137 0.01 4.91124e-06 0.001
Iteration 80: LL = -4115.76

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0216089 0.0216591 0.0216168 0.0234677 0.0216047 0.0216029 0.0221142 0.542 0.0223031 0.0216029 0.0218261 0.0216446 0.0215987 0.0216108 0.0221426 0.0216289 0.0216029 0.0219183 0.0216277 0.0216108 0.0216059 0.0216029 
0.0199229 0.01 4.8406e-06 0.001
Iteration 81: LL = -4115.74

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.021441 0.0214908 0.0214488 0.0232853 0.0214368 0.021435 0.0219424 0.545559 0.0221298 0.021435 0.0216564 0.0214764 0.0214308 0.0214428 0.0219705 0.0214608 0.021435 0.021748 0.0214596 0.0214428 0.021438 0.021435 
0.0196381 0.01 4.77144e-06 0.001
Iteration 82: LL = -4115.72

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0212743 0.0213238 0.0212821 0.0231044 0.0212702 0.0212684 0.0217718 0.549091 0.0219578 0.0212684 0.0214881 0.0213094 0.0212642 0.0212761 0.0217998 0.021294 0.0212684 0.0215789 0.0212928 0.0212761 0.0212714 0.0212684 
0.0193593 0.01 4.70371e-06 0.001
Iteration 83: LL = -4115.7

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.021109 0.021158 0.0211167 0.0229248 0.0211049 0.0211031 0.0216026 0.552596 0.0217871 0.0211031 0.0213211 0.0211438 0.021099 0.0211108 0.0216303 0.0211285 0.0211031 0.0214112 0.0211273 0.0211108 0.021106 0.0211031 
0.0190861 0.01 4.63737e-06 0.001
Iteration 84: LL = -4115.68

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0209449 0.0209936 0.0209526 0.0227466 0.0209408 0.0209391 0.0214347 0.556073 0.0216178 0.0209391 0.0211554 0.0209795 0.020935 0.0209467 0.0214622 0.0209643 0.0209391 0.0212448 0.0209631 0.0209467 0.020942 0.0209391 
0.0188185 0.01 4.57237e-06 0.001
Iteration 85: LL = -4115.67

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0207822 0.0208304 0.0207897 0.0225698 0.0207781 0.0207763 0.0212681 0.559523 0.0214498 0.0207763 0.020991 0.0208164 0.0207723 0.0207839 0.0212954 0.0208014 0.0207763 0.0210797 0.0208002 0.0207839 0.0207792 0.0207763 
0.0185563 0.01 4.50868e-06 0.001
Iteration 86: LL = -4115.65

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0206206 0.0206685 0.0206281 0.0223944 0.0206166 0.0206149 0.0211028 0.562946 0.0212831 0.0206149 0.0208278 0.0206547 0.0206108 0.0206224 0.0211299 0.0206397 0.0206149 0.0209159 0.0206385 0.0206224 0.0206178 0.0206149 
0.0182993 0.01 4.44626e-06 0.001
Iteration 87: LL = -4115.63

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0204604 0.0205079 0.0204678 0.0222204 0.0204564 0.0204547 0.0209388 0.566343 0.0211177 0.0204547 0.020666 0.0204941 0.0204506 0.0204621 0.0209657 0.0204793 0.0204547 0.0207533 0.0204781 0.0204621 0.0204575 0.0204547 
0.0180474 0.01 4.38508e-06 0.001
Iteration 88: LL = -4115.61

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0203014 0.0203485 0.0203087 0.0220477 0.0202974 0.0202957 0.0207761 0.569714 0.0209535 0.0202957 0.0205053 0.0203349 0.0202917 0.0203031 0.0208028 0.0203201 0.0202957 0.020592 0.0203189 0.0203031 0.0202985 0.0202957 
0.0178005 0.01 4.3251e-06 0.001
Iteration 89: LL = -4115.59

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0201436 0.0201904 0.0201509 0.0218763 0.0201396 0.0201379 0.0206146 0.573058 0.0207907 0.0201379 0.020346 0.0201768 0.020134 0.0201453 0.0206411 0.0201622 0.0201379 0.020432 0.020161 0.0201453 0.0201408 0.0201379 
0.0175584 0.01 4.26629e-06 0.001
Iteration 90: LL = -4115.58

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.019987 0.0200334 0.0199943 0.0217063 0.0199831 0.0199814 0.0204544 0.576376 0.0206291 0.0199814 0.0201878 0.02002 0.0199775 0.0199887 0.0204806 0.0200055 0.0199814 0.0202732 0.0200043 0.0199887 0.0199842 0.0199814 
0.0173209 0.01 4.20861e-06 0.001
Iteration 91: LL = -4115.56

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0198317 0.0198777 0.0198389 0.0215376 0.0198278 0.0198261 0.0202954 0.579668 0.0204688 0.0198261 0.0200309 0.0198644 0.0198222 0.0198334 0.0203215 0.01985 0.0198261 0.0201156 0.0198489 0.0198334 0.0198289 0.0198261 
0.017088 0.01 4.15204e-06 0.001
Iteration 92: LL = -4115.54

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0196775 0.0197232 0.0196847 0.0213702 0.0196737 0.019672 0.0201377 0.582935 0.0203097 0.019672 0.0198753 0.01971 0.0196682 0.0196792 0.0201635 0.0196957 0.019672 0.0199593 0.0196946 0.0196792 0.0196748 0.019672 
0.0168596 0.01 4.09655e-06 0.001
Iteration 93: LL = -4115.53

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0195246 0.01957 0.0195317 0.0212041 0.0195208 0.0195192 0.0199812 0.586177 0.0201519 0.0195192 0.0197208 0.0195568 0.0195153 0.0195263 0.0200068 0.0195427 0.0195192 0.0198041 0.0195415 0.0195263 0.0195219 0.0195192 
0.0166354 0.01 4.0421e-06 0.001
Iteration 94: LL = -4115.51

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0193729 0.0194179 0.0193799 0.0210393 0.0193691 0.0193674 0.0198259 0.589393 0.0199952 0.0193674 0.0195675 0.0194048 0.0193637 0.0193745 0.0198513 0.0193908 0.0193674 0.0196502 0.0193897 0.0193745 0.0193702 0.0193674 
0.0164155 0.01 3.98866e-06 0.001
Iteration 95: LL = -4115.49

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0192223 0.0192669 0.0192293 0.0208758 0.0192185 0.0192169 0.0196718 0.592584 0.0198398 0.0192169 0.0194154 0.019254 0.0192132 0.0192239 0.019697 0.0192401 0.0192169 0.0194975 0.019239 0.0192239 0.0192196 0.0192169 
0.0161996 0.01 3.93623e-06 0.001
Iteration 96: LL = -4115.48

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0190729 0.0191172 0.0190798 0.0207135 0.0190692 0.0190676 0.0195189 0.595751 0.0196856 0.0190676 0.0192646 0.0191044 0.0190638 0.0190745 0.019544 0.0190905 0.0190676 0.019346 0.0190894 0.0190745 0.0190702 0.0190676 
0.0159877 0.01 3.88475e-06 0.001
Iteration 97: LL = -4115.46

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0189247 0.0189686 0.0189316 0.0205526 0.018921 0.0189194 0.0193672 0.598892 0.0195326 0.0189194 0.0191148 0.0189559 0.0189157 0.0189263 0.0193921 0.0189422 0.0189194 0.0191956 0.0189411 0.0189263 0.018922 0.0189194 
0.0157797 0.01 3.83422e-06 0.001
Iteration 98: LL = -4115.45

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0187776 0.0188212 0.0187844 0.0203928 0.0187739 0.0187723 0.0192167 0.60201 0.0193808 0.0187723 0.0189663 0.0188086 0.0187687 0.0187792 0.0192413 0.0187949 0.0187723 0.0190464 0.0187939 0.0187792 0.018775 0.0187723 
0.0155754 0.01 3.78461e-06 0.001
Iteration 99: LL = -4115.43

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0186316 0.0186749 0.0186384 0.0202343 0.018628 0.0186264 0.0190673 0.605103 0.0192302 0.0186264 0.0188189 0.0186624 0.0186228 0.0186332 0.0190918 0.0186489 0.0186264 0.0188984 0.0186478 0.0186332 0.018629 0.0186264 
0.0153748 0.01 3.73589e-06 0.001
Iteration 100: LL = -4115.42

	IN_FRAME [P_GEOM(rep)=0.945369, P_DOWN=0.024093, P_UP=0.00132531]
	OUT_FRAME[P_GEOM(bp) =0.230494, P_DOWN=0.00710874, P_UP=0.0255957]
Pop freqs: 0.0184868 0.0185298 0.0184936 0.0200771 0.0184832 0.0184817 0.0189191 0.608172 0.0190807 0.0184817 0.0186726 0.0185173 0.0184781 0.0184884 0.0189434 0.0185039 0.0184817 0.0187515 0.0185029 0.0184884 0.0184843 0.0184817 
0.0151779 0.01 3.68804e-06 0.001
Stutter model training failed for locus 21:45056084-45056150 with 11561 informative reads
Locus timing:
 BAM seek time       = 1.1e-05 seconds
 Read filtering      = 1.03949 seconds
 SNP info extraction = 0.033535 seconds
 Stutter estimation  = 54.2648 seconds




------HipSTR Execution Summary------
Stutter model training succeeded for 0/1 loci
Genotyping succeeded for 0/0 loci

Approximate timing breakdown
 BAM seek time       = 1.1e-05 seconds
 Read filtering      = 1.03949 seconds
 SNP info extraction = 0.033535 seconds
 Stutter estimation  = 54.2648 seconds
 Genotyping          = 6e-06 seconds
	 Left alignment        = 0 seconds
	 Haplotype generation  = 0 seconds
	 Haplotype alignment   = 0 seconds
	 Flank assembly        = 0 seconds
	 Posterior computation = 0 seconds
	 Alignment traceback   = 0 seconds
HipSTR execution finished: Total runtime = 55.7189 sec
-----------------

The text was updated successfully, but these errors were encountered:

tfwillems · 2017-11-11T19:17:31Z

@nh13
Hi Nils,

Thanks for sharing these details. Looking at the parameters printed during each iteration, it looks like you've uncovered a bug in the EM procedure. Each of the population frequencies should be between 0 and 1, but there's some crazy numbers like 1.79769e+308 and 3071.9. In addition to this being an obvious bug, I suspect this issue is likely playing a role in the slow convergence.

Could you send me the required files to reproduce this issue? I'm optimistic that if I can debug on my end, it'll resolve the bug and the convergence issues. If the convergence issues remain after the bug fix, I think it makes sense to relax the stringency of the convergence criteria.

Thanks!
Thomas

nh13 · 2017-11-13T17:48:57Z

@tfwillems I have send you some tests cases for this issue via email. Please let me know if you did not receive them.

nh13 · 2017-11-13T17:57:12Z

I also forgot to say that I saw a lot of very small probabilities, and so you may want to look at using log1p instead of log and expm1 instead of exp as they sometimes are more precise. A good reference for such implementations is in this R note. We found this helpful to implement in fgbio (see here).

tfwillems · 2017-11-13T18:07:04Z

Great @nh13, I'll dig into these when I get and chance and see whether the above suggestions are also helpful

tfwillems · 2017-11-21T02:13:12Z

Hi @nh13,
I took a look at the examples you sent. I previously misinterpreted the logging output you sent my way. It turns out there was no bug, as each iteration two lines were logged and the second line doesn't pertain to the EM parameters and indicates the change in likelihood. So to make a long story short, it just looks like the likelihood at these loci changes very slowly, even though the stutter model parameters don't really change.

To address these cases, I've modified the EM procedure such that it triggers convergence if the parameters haven't changed since the last iteration. The resulting changes were added in commit df53cb0. This fixes the cases you sent and hopefully no future cases will arise.

Best,
Thomas

tfwillems mentioned this issue Nov 11, 2017

Best way to debug when the stutter model fails to train? #35

Closed

tfwillems self-assigned this Nov 11, 2017

tfwillems added the bug label Nov 11, 2017

tfwillems closed this as completed Nov 21, 2017

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Stutter model failed to converge at a site #46

Stutter model failed to converge at a site #46

nh13 commented Nov 8, 2017

tfwillems commented Nov 11, 2017

nh13 commented Nov 13, 2017

nh13 commented Nov 13, 2017

tfwillems commented Nov 13, 2017

tfwillems commented Nov 21, 2017

Stutter model failed to converge at a site #46

Stutter model failed to converge at a site #46

Comments

nh13 commented Nov 8, 2017

tfwillems commented Nov 11, 2017

nh13 commented Nov 13, 2017

nh13 commented Nov 13, 2017

tfwillems commented Nov 13, 2017

tfwillems commented Nov 21, 2017