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tfwillems / HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
GNU General Public License v2.0
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Stutter model failed to converge at a site #46

Closed nh13 closed 6 years ago

nh13 commented 6 years ago

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 ----------------- ```
tfwillems commented 6 years ago

@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 commented 6 years ago

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

nh13 commented 6 years ago

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 commented 6 years ago

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

tfwillems commented 6 years ago

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 df53cb03943c0dd77992055da9c08807b9f45f8b. This fixes the cases you sent and hopefully no future cases will arise.

Best, Thomas