Mach 1.0.18.c -- Markov Chain Haplotyping
(c) 2005-2007 Goncalo Abecasis, with thanks to Yun Li, Paul Scheet


The following parameters are in effect:

Available Options
        Input Files : --datfile [myers22.dat], --pedfile [myers22.ped],
                      --mask [0.00]
     Optional Files : --crossoverMap [], --errorMap [], --physicalMap []
        Phased Data : --snps [], --haps [], --hapmapFormat, --vcfReference,
                      --autoFlip, --greedy
   Regional Options : --startposition [0.00], --endposition [300000000.00]
     Markov Sampler : --seed [123456], --burnin, --rounds [20]
    Mapping Options : --npl, --association
         Haplotyper : --states [200], --errorRate [1.0e-03], --weighted,
                      --compact
         Imputation : --forceImputation, --geno, --quality, --dosage, --probs,
                      --mle
       Output Files : --prefix [myers22.haps], --phase [ON], --uncompressed,
                      --mldetails
     Interim Output : --sampleInterval [5], --interimInterval [5]

WARNING: no reference haplotypes provided.
Count number of markers in the sample marker information file ...
  Read 5405 markers from sample marker information file
Loaded pedigree with:
    193 individuals to be haplotyped at 5405 markers

Formating genotypes and allocating memory for haplotyping
                          Pedigree file ... 3.0 mb
               Haplotyping engine (max) ... 418.7 mb
            Haplotyping engine (actual) ... 416.4 mb
                      Consensus builder ... 8.0 mb
Memory allocated successfully

Found initial haplotype set

Markov Chain iteration 1 [63888 mosaic crossovers]
Merged sampled haplotypes to generate consensus
   Consensus estimated to have 0.0 errors in missing genotypes and 0.0 flips in haplotypes

Wrote out file [myers22.haps.prelim1.gz] with phased chromosomes ...
Wrote out file [myers22.haps.prelim.1.rec] with mosaic crossover rates ...
Wrote out file [myers22.haps.prelim.1.erate] with per marker error rates ...

Wrote out file [myers22.haps.sample1] with phased chromosomes ...
Markov Chain iteration 2 [72563 mosaic crossovers]
Markov Chain iteration 3 [77366 mosaic crossovers]
Markov Chain iteration 4 [80657 mosaic crossovers]
Markov Chain iteration 5 [82339 mosaic crossovers]
Markov Chain iteration 6 [84515 mosaic crossovers]
Merged sampled haplotypes to generate consensus
   Consensus estimated to have 4194.3 errors in missing genotypes and 28377.0 flips in haplotypes

Wrote out file [myers22.haps.prelim6.gz] with phased chromosomes ...
Wrote out file [myers22.haps.prelim.6.rec] with mosaic crossover rates ...
Wrote out file [myers22.haps.prelim.6.erate] with per marker error rates ...

Wrote out file [myers22.haps.sample6] with phased chromosomes ...
Markov Chain iteration 7 [86322 mosaic crossovers]
Markov Chain iteration 8 [87430 mosaic crossovers]
Markov Chain iteration 9 [88459 mosaic crossovers]
Markov Chain iteration 10 [89511 mosaic crossovers]
Markov Chain iteration 11 [90161 mosaic crossovers]
Merged sampled haplotypes to generate consensus
   Consensus estimated to have 4218.5 errors in missing genotypes and 29083.8 flips in haplotypes

Wrote out file [myers22.haps.prelim11.gz] with phased chromosomes ...
Wrote out file [myers22.haps.prelim.11.rec] with mosaic crossover rates ...
Wrote out file [myers22.haps.prelim.11.erate] with per marker error rates ...

Wrote out file [myers22.haps.sample11] with phased chromosomes ...
Markov Chain iteration 12 [90693 mosaic crossovers]
Markov Chain iteration 13 [91253 mosaic crossovers]
Markov Chain iteration 14 [91506 mosaic crossovers]
Markov Chain iteration 15 [91654 mosaic crossovers]
Markov Chain iteration 16 [91812 mosaic crossovers]
Merged sampled haplotypes to generate consensus
   Consensus estimated to have 4205.2 errors in missing genotypes and 29784.5 flips in haplotypes

Wrote out file [myers22.haps.prelim16.gz] with phased chromosomes ...
Wrote out file [myers22.haps.prelim.16.rec] with mosaic crossover rates ...
Wrote out file [myers22.haps.prelim.16.erate] with per marker error rates ...

Wrote out file [myers22.haps.sample16] with phased chromosomes ...
Markov Chain iteration 17 [92002 mosaic crossovers]
Markov Chain iteration 18 [91769 mosaic crossovers]
Markov Chain iteration 19 [91877 mosaic crossovers]
Markov Chain iteration 20 [91817 mosaic crossovers]

Merged sampled haplotypes to generate consensus
   Consensus estimated to have 4185.9 errors in missing genotypes and 30014.2 flips in haplotypes

Wrote out file [myers22.haps.gz] with phased chromosomes ...
Wrote out file [myers22.haps.rec] with mosaic crossover rates ...
Wrote out file [myers22.haps.erate] with per marker error rates ...

Estimated mismatch rate in Markov model is: 0.00140

Analysis took 4023 seconds