
The following parameters are in effect:
                     Data File : .\temp\temp.dat (-dname)
                 Pedigree File : .\temp\temp.ped (-pname)
            Missing Value Code :         -99.999 (-xname)
                      Map File : .\temp\temp.map (-mname)
            Allele Frequencies : .\temp\temp.freq (-f[a|e|f|m|file])
                   Random Seed :          123456 (-r9999)

Data Analysis Options
         General : --error, --information, --likelihood [ON],
                   --model [param.tbl]
          Errors : --flag, --perAllele [0.00], --perGenotype [0.00], --fit
      IBD States : --ibd, --kinship, --matrices, --select
     NPL Linkage : --npl, --pairs, --qtl, --deviates, --exp
      VC Linkage : --vc, --useCovariates, --ascertainment, --unlinked [0.00]
     Association : --infer, --assoc, --fastAssoc, --filter, --custom [cov.tbl]
     Haplotyping : --best, --sample, --all, --founders, --horizontal
   Recombination : --zero, --one, --two, --three, --singlepoint
       Positions : --steps, --maxStep, --minStep, --grid, --start, --stop
     LD Clusters : --clusters [.\temp\temp.clusters], --distance, --rsq,
                   --cfreq
          Limits : --bits [24], --megabytes, --minutes
     Performance : --trim, --swap, --smallSwap
          Output : --quiet [ON], --markerNames, --frequencies,
                   --perFamily [ON], --pdf, --tabulate, --prefix [merlin]
      Simulation : --simulate, --reruns, --save, --trait []

MARKER CLUSTERS: Marker map changed, see [merlin-clusters.log]
MARKER CLUSTERS: User supplied file defines 1 cluster

Family:     1 - Founders: 2  - Descendants: 2  - Bits: 1 
  lnLikelihood = -9.48096752474128120000    

Family:     2 - Founders: 3  - Descendants: 2  - Bits: 1 
  lnLikelihood = -13.88097892003266100000    

Family:     3 - Founders: 3  - Descendants: 2  - Bits: 0 
  lnLikelihood = -13.20003418587413800000

Family:     4 - Founders: 2  - Descendants: 0  - Bits: 0 
  lnLikelihood = -17.60004558116551700000


lnLikelihood for 4 families (0 skipped) = -54.16202621181359700000



