Mach 1.0.16 -- 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 [sample2.dat], --pedfile [sample2.ped],
                     --mask [0.02]
    Optional Files : --crossoverMap [], --errorMap [], --physicalMap []
       Phased Data : --snps [hapmap.snps], --haps [hapmap.haplos],
                     --hapmapFormat, --autoFlip, --greedy [ON]
    Markov Sampler : --seed [123456], --burnin, --rounds [20]
   Mapping Options : --npl, --association
        Haplotyper : --states, --errorRate [1.0e-03], --weighted, --compact
        Imputation : --geno, --quality, --dosage, --probs, --mle
      Output Files : --prefix [mask], --phase, --mldetails
    Interim Output : --sampleInterval, --interimInterval

Loading list of markers in phased haplotype ...
Loading phased haplotypes ...

   GREEDY SOLUTION. Phased haplotypes will be used to resolve ambiguous
   individuals and generate a greedy solution.

Loaded pedigree with:
    500 individuals to be haplotyped at 178 markers
    2% of genotypes will be masked prior to haplotyping

Formating genotypes and allocating memory for haplotyping
                          Pedigree file ... 247.1 kb
                 Phase known haplotypes ... 21.9 kb
               Haplotyping engine (max) ... 6.2 mb
            Haplotyping engine (actual) ... 2.6 mb
                      Dosage Calculator ... 174.8 kb
Memory allocated successfully

Found initial haplotype set

Markov Chain iteration 1 [2034 mosaic crossovers]
Markov Chain iteration 2 [2119 mosaic crossovers]
Markov Chain iteration 3 [2214 mosaic crossovers]
Markov Chain iteration 4 [2309 mosaic crossovers]
Markov Chain iteration 5 [2333 mosaic crossovers]
Markov Chain iteration 6 [2396 mosaic crossovers]
Markov Chain iteration 7 [2390 mosaic crossovers]
Markov Chain iteration 8 [2445 mosaic crossovers]
Markov Chain iteration 9 [2482 mosaic crossovers]
Markov Chain iteration 10 [2469 mosaic crossovers]
Markov Chain iteration 11 [2482 mosaic crossovers]
Markov Chain iteration 12 [2451 mosaic crossovers]
Markov Chain iteration 13 [2513 mosaic crossovers]
Markov Chain iteration 14 [2535 mosaic crossovers]
Markov Chain iteration 15 [2532 mosaic crossovers]
Markov Chain iteration 16 [2515 mosaic crossovers]
Markov Chain iteration 17 [2526 mosaic crossovers]
Markov Chain iteration 18 [2588 mosaic crossovers]
Markov Chain iteration 19 [2540 mosaic crossovers]
Markov Chain iteration 20 [2543 mosaic crossovers]

Wrote out file [mask.info] with marker information
Wrote out file [mask.rec] with mosaic crossover rates ...
Wrote out file [mask.erate] with per marker error rates ...

Comparing 481 masked genotypes with estimates ...
   Estimated per genotype error rate is  0.0624
   Estimated per allele error rate is 0.0312

Estimated mismatch rate in Markov model is: 0.00000