MORGAN Version 3.0.2 ./lmlink Thu Jul 7 11:17:58 2011 === Parsing of parameter statements completed === Chromosome map .............. Inter-locus distances in cM, using Haldane map function: ---------------------------------------------------------------- 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 +------+------+------+------+------+------+------+------+------+ M1 M2 M3 M4 M5 M6 M7 M8 M9 M10 T1 test positions (cM): T T T T T +------+------+------+------+------- 34.7 34.7 28.0 12.6 5.3 -----------------------------------+ M1 T T -------+------+------- 3.0 4.0 3.0 +--------------------+ M1 M2 T T -------+------+------- 3.0 4.0 3.0 +--------------------+ M2 M3 T T -------+------+------- 3.0 4.0 3.0 +--------------------+ M3 M4 T T -------+------+------- 3.0 4.0 3.0 +--------------------+ M4 M5 T T -------+------+------- 3.0 4.0 3.0 +--------------------+ M5 M6 T T -------+------+------- 3.0 4.0 3.0 +--------------------+ M6 M7 T T -------+------+------- 3.0 4.0 3.0 +--------------------+ M7 M8 T T -------+------+------- 3.0 4.0 3.0 +--------------------+ M8 M9 T T -------+------+------- 3.0 4.0 3.0 +--------------------+ M9 M10 T T T T T -------+------+------+------+------+ 5.3 12.6 28.0 34.7 34.7 +----------------------------------- M10 Marker allele frequencies: M1 .130 .660 .160 .050 M2 .060 .230 .410 .250 .050 M3 .110 .020 .010 .060 .240 .560 M4 .070 .040 .890 M5 .120 .110 .030 .030 .500 .210 M6 .500 .440 .060 M7 .010 .330 .620 .040 M8 .200 .050 .420 .270 .060 M9 .180 .180 .250 .160 .080 .150 M10 .170 .350 .040 .290 .150 Tloc allele frequencies: T1 .400 .600 Marker data: M1 M2 M3 M4 M5 M6 M7 M8 M9 M10 302 2 2 3 3 6 6 3 3 1 5 1 1 3 3 2 4 1 2 2 3 306 2 3 3 5 1 6 3 3 5 6 1 3 2 3 1 2 2 6 5 5 307 2 2 3 3 4 6 3 3 5 5 1 2 2 3 2 4 2 2 4 5 404 0 0 2 3 5 6 3 3 2 5 1 2 0 0 1 4 6 6 4 5 406 2 2 2 3 6 6 3 3 5 6 2 2 3 3 3 4 1 3 2 4 407 2 2 2 3 2 6 3 3 1 5 1 2 3 3 1 4 1 3 2 4 408 2 2 2 3 2 6 3 3 1 5 1 2 3 3 4 4 1 1 2 3 410 2 2 3 4 1 6 3 3 1 6 2 3 2 4 4 5 4 4 0 0 411 2 3 4 5 1 6 3 3 1 6 1 3 2 4 4 5 4 4 4 5 412 2 3 4 5 1 6 3 3 1 6 2 3 2 3 2 4 2 4 4 5 414 2 3 2 5 1 5 3 3 5 5 2 2 3 3 1 4 3 6 3 5 415 2 2 2 3 5 6 3 3 5 5 1 2 3 3 1 1 3 6 2 5 416 3 3 3 5 1 6 0 0 5 5 2 2 2 3 2 4 2 3 3 5 505 1 2 3 3 5 6 3 3 5 6 1 1 0 0 1 2 6 6 4 5 506 1 2 2 3 5 6 1 3 2 5 1 2 2 2 2 4 6 6 4 4 507 1 2 2 3 5 5 3 3 5 6 0 0 3 3 0 0 6 6 4 5 508 1 2 3 3 6 6 1 3 5 6 1 1 3 3 1 3 1 6 2 5 509 2 2 2 3 5 6 3 3 1 5 2 2 2 3 0 0 0 0 3 3 510 2 2 2 3 5 6 3 3 6 6 1 2 3 3 3 4 1 4 3 3 511 2 2 2 3 5 6 3 3 6 6 1 2 3 3 3 4 1 3 3 4 512 2 2 2 2 6 6 3 3 1 5 2 2 2 3 1 1 3 4 2 3 513 1 2 3 4 1 2 0 0 5 5 1 2 3 3 3 4 0 0 2 3 514 1 2 2 4 1 6 3 3 1 5 0 0 3 3 2 4 1 5 2 2 516 1 2 3 4 0 0 3 3 5 5 2 2 3 3 3 4 1 3 2 3 601 2 2 3 3 6 6 3 3 5 5 1 2 2 3 1 4 4 6 1 5 5150 1 2 2 5 5 6 3 3 3 5 2 2 0 0 3 4 1 1 1 1 602 2 3 2 3 1 6 3 3 3 5 2 2 0 0 4 4 1 1 1 2 1301 2 2 2 3 6 6 0 0 5 5 1 2 3 3 1 3 3 6 1 4 1302 2 2 2 3 6 6 3 3 5 5 1 2 3 3 1 3 5 6 4 5 1303 1 2 0 0 1 6 1 3 5 6 1 1 3 3 1 3 3 6 2 4 1304 2 3 2 3 5 6 3 3 5 6 2 3 3 4 0 0 3 6 2 5 1305 2 3 2 3 5 6 3 3 3 5 2 3 3 4 3 3 3 6 1 5 2301 2 2 3 4 6 6 1 3 5 5 2 2 3 3 1 4 1 3 2 2 2302 2 3 3 4 6 6 3 3 2 5 1 2 2 3 2 5 3 6 2 2 2306 2 2 3 3 6 6 3 3 5 6 2 2 3 3 3 5 1 2 2 2 2307 2 2 3 4 1 6 0 0 5 5 1 2 3 3 3 5 1 2 2 2 2308 2 2 4 4 1 6 3 3 5 5 1 2 3 3 3 5 1 3 2 4 2303 2 4 3 4 1 5 2 3 5 5 1 2 2 3 3 4 0 0 1 2 2304 1 2 4 4 1 1 0 0 3 5 1 2 2 3 3 4 0 0 1 2 2305 2 4 3 4 1 5 2 3 5 5 2 2 3 3 4 4 2 6 1 2 Trait data are discrete Discrete data at trait locus are to be read from integer 4 in the pedigree record Incomplete penetrances for the trait are: genotype code penetrance -------- ---- ---------- (1 1) 0 0.050 (1 2), (2 1) 1 0.600 (2 2) 2 0.950 Multiple meiosis sampler is to be used with L-sampler probability set to 0.200 Sequential imputation to be used for setup, using 300 samples Sampling is to be by scan, with scores estimated every scan MCMC is being done globally over all components The number of MC burn-in iterations is 150 Number of MC iterations requested is 3000 with progress checked every 1000 iterations Number of batches for MC variance estimation is 20 === Checking of parameter statements completed === Opened input pedigree file "../ped73.ped" 73 individuals read Pedigree component information: compnt size founders females males first 1 47 13 25 22 101 2 11 4 6 5 1101 3 15 5 7 8 2101 total 73 22 38 35 === Checking of pedigree file completed === Opened input pedigree file "../ped73.ped" Pedigree records contain: names, 6 integers, 1 real number The number of meiosis switches to sample is 99 compnt switches first last 1 65 1 65 2 14 66 79 3 20 80 99 Trait data: Component 1: phenotype 2: 302 307 406 407 408 411 414 416 505 507 508 511 512 513 514 516 601 602 phenotype 1: 306 404 410 412 415 506 509 510 5150 Component 2: phenotype 2: 1301 1303 1304 phenotype 1: 1302 1305 Component 3: phenotype 2: 2301 2302 2306 2307 2308 2305 phenotype 1: 2303 2304 Genetic variables in the analysis: index name type 0 trt-pheno discrete 1 marker-1 geno-marker 2 marker-2 geno-marker 3 marker-3 geno-marker 4 marker-4 geno-marker 5 marker-5 geno-marker 6 marker-6 geno-marker 7 marker-7 geno-marker 8 marker-8 geno-marker 9 marker-9 geno-marker 10 marker-10 geno-marker Hexadecimal sampler seeds: 0x7aadfd2d 0xae234ab1 === Setup for MCMC completed === === Inheritance indicators initialized using sequential imputation === === Setup for marriage structure completed === 3000 realizations will be scored, at scoring interval 1 Scored realizations will be batched in 20 sets of size 150 Base log-likelihood log_10 P(Y_T) = -1.136373e+01 === MCMC sampling begun === Now starting 150 iterations of burn-in Now starting 3000 iterations of MCMC Starting M-sampler iteration 1000 Starting M-sampler iteration 2000 Starting M-sampler iteration 3000 === MCMC sampling completed === Summary for component 1: Average total log-probability of segregations: for first locus (constant): -45.055 for each successive locus: -16.382 -19.383 -18.832 -21.188 -18.771 -22.345 -19.732 -15.691 -16.570 Average total log-probability of penetrances, by locus: marker-1 marker-2 marker-3 marker-4 marker-5 marker-6 marker-7 marker-8 marker-9 marker-10 -18.745 -27.081 -25.731 -4.880 -27.283 -18.492 -15.948 -38.345 -39.085 -35.363 Recombination counts for map intervals: males: females: total recomb non-rec total recomb non-rec 1, 2 99000 5346 93654 96000 7933 88067 2, 3 99000 11337 87663 96000 5846 90154 3, 4 99000 8789 90211 96000 7677 88323 4, 5 99000 11828 87172 96000 7703 88297 5, 6 99000 7824 91176 96000 8563 87437 6, 7 99000 10320 88680 96000 10717 85283 7, 8 99000 12689 86311 96000 4948 91052 8, 9 99000 4720 94280 96000 7660 88340 9, 10 99000 6203 92797 96000 7320 88680 Summary for component 2: Average total log-probability of segregations: for first locus (constant): -9.704 for each successive locus: -3.422 -3.338 -3.735 -4.895 -5.566 -3.585 -4.083 -4.863 -4.525 Average total log-probability of penetrances, by locus: marker-1 marker-2 marker-3 marker-4 marker-5 marker-6 marker-7 marker-8 marker-9 marker-10 -4.760 -3.569 -5.028 -2.934 -7.638 -5.393 -4.996 -5.400 -10.246 -9.802 Recombination counts for map intervals: males: females: total recomb non-rec total recomb non-rec 1, 2 21000 1505 19495 21000 1216 19784 2, 3 21000 1411 19589 21000 1201 19799 3, 4 21000 1519 19481 21000 1610 19390 4, 5 21000 1853 19147 21000 2785 18215 5, 6 21000 2237 18763 21000 3274 17726 6, 7 21000 1380 19620 21000 1554 19446 7, 8 21000 1569 19431 21000 2012 18988 8, 9 21000 2417 18583 21000 2179 18821 9, 10 21000 1570 19430 21000 2586 18414 Summary for component 3: Average total log-probability of segregations: for first locus (constant): -13.863 for each successive locus: -5.718 -5.353 -5.434 -5.349 -6.926 -5.773 -5.789 -10.016 -6.029 Average total log-probability of penetrances, by locus: marker-1 marker-2 marker-3 marker-4 marker-5 marker-6 marker-7 marker-8 marker-9 marker-10 -8.958 -9.760 -10.241 -6.004 -11.053 -6.429 -5.203 -12.991 -11.374 -8.804 Recombination counts for map intervals: males: females: total recomb non-rec total recomb non-rec 1, 2 30000 2723 27277 30000 2244 27756 2, 3 30000 2015 27985 30000 2477 27523 3, 4 30000 2170 27830 30000 2427 27573 4, 5 30000 2050 27950 30000 2437 27563 5, 6 30000 2072 27928 30000 4467 25533 6, 7 30000 2459 27541 30000 2579 27421 7, 8 30000 2367 27633 30000 2692 27308 8, 9 30000 3805 26195 30000 6754 23246 9, 10 30000 2294 27706 30000 3077 26923 === LodScore for all the components completed === LodScore estimates by Rao-Blackwellized computation: Trait pos # position (Haldane cM) or marker male female LodScore StdErr 1 -115.129 -115.129 -0.0062 0.0002 2 -80.472 -80.472 -0.0162 0.0004 3 -45.815 -45.815 -0.0557 0.0014 4 -17.834 -17.834 -0.1934 0.0045 5 -5.268 -5.268 -0.3614 0.0089 marker-1 0.000 0.000 -0.4729 0.0126 6 3.000 3.000 -0.4794 0.0105 7 7.000 7.000 -0.5040 0.0109 marker-2 10.000 10.000 -0.5377 0.0143 8 13.000 13.000 -0.5259 0.0112 9 17.000 17.000 -0.5286 0.0105 marker-3 20.000 20.000 -0.5480 0.0130 10 23.000 23.000 -0.3723 0.0109 11 27.000 27.000 -0.2059 0.0105 marker-4 30.000 30.000 -0.1143 0.0115 12 33.000 33.000 0.0343 0.0099 13 37.000 37.000 0.1883 0.0099 marker-5 40.000 40.000 0.2758 0.0122 14 43.000 43.000 0.3832 0.0104 15 47.000 47.000 0.4937 0.0095 marker-6 50.000 50.000 0.5575 0.0102 16 53.000 53.000 0.4414 0.0087 17 57.000 57.000 0.2624 0.0099 marker-7 60.000 60.000 0.1028 0.0127 18 63.000 63.000 0.0346 0.0106 19 67.000 67.000 -0.0860 0.0087 marker-8 70.000 70.000 -0.2133 0.0085 20 73.000 73.000 -0.1523 0.0070 21 77.000 77.000 -0.1149 0.0061 marker-9 80.000 80.000 -0.1171 0.0059 22 83.000 83.000 -0.0440 0.0045 23 87.000 87.000 0.0339 0.0051 marker-10 90.000 90.000 0.0828 0.0073 24 95.268 95.268 0.1711 0.0052 25 107.834 107.834 0.1955 0.0029 26 135.815 135.815 0.1100 0.0010 27 170.472 170.472 0.0439 0.0003 28 205.129 205.129 0.0180 0.0001 Opened output seed file "../sampler.seed" hostname: madrid1 system time: 0.010 sec user time: 89.930 sec elapsed time: 0 hr 1 min 30 sec