
===================================================================
  Welcome to HAPGEN_v2.2.0 (01/04/2011)
  Zhan Su, Peter Donnelly, Jonathan Marchini
===================================================================

Command line input is:
hapgen2 -m /homes/hannah/data/hmeyer/Supplementary/CEU.0908.impute.files/genetic_map_chr22_combined_b36.txt -l legend_file -h /homes/hannah/data/hmeyer/Supplementary/CEU.0908.impute.files/CEU.0908.chr22.hap -o genotypes_hapgen -n 100 0 -dl 45162 0 0 0 -no_haps_output 

FILE INPUTS
                                            haplotype file: /homes/hannah/data/hmeyer/Supplementary/CEU.0908.impute.files/CEU.0908.chr22.hap
                                               legend file: legend_file
                                          genetic map file: /homes/hannah/data/hmeyer/Supplementary/CEU.0908.impute.files/genetic_map_chr22_combined_b36.txt
                                             tag snps file: 
FILE OUTPUTS
                                               output file: genotypes_hapgen
                                              summary file: genotypes_hapgen.summary
PARAMETER INPUTS
                                  no. controls to simulate: 100
                                     no. cases to simulate: 0
                                              disease loci: (1) 45162 
                                           disease alleles: (1) 0 
                             heterozygote/homozygote risks: (1) 0.00/0.00 
                                                     lower: 0
                                                     upper: 500000000
                                                        Ne: 11418
                                                     theta: -1

Reading genetic map file ... done
                                      number of rates read: 43414


Reading haplotype and legend files: looking for SNPs in [0, 500000000] ... done
                                      number of haplotypes: 112
                                   number of SNPs in total: 1000
                                number of SNPs in interval: 1000


Random seed set to 0.889133
theta not set, so setting to a default value of 0.188673

Processing disease loci ... done 


Simulating haplotypes ... done

Writing output to files 
writing output file genotypes_hapgen.controls.gen
writing output file genotypes_hapgen.cases.gen
writing output file genotypes_hapgen.controls.sample
writing output file genotypes_hapgen.cases.sample

HAPGEN took 0 seconds to complete. Have a nice day! 
