IMPUTE2 – problem with MCMC

IMPUTE2 – problem with MCMC

1

Dear,
I’ve run an imputation using the fallowing command

Impute -use_prephased_g -known_haps_g output_phased.haps -h 1000GP_Phase3.hap.gz -l 1000GP_Phase3.legend.gz -m genetic_map.txt -int 1 1000000 -iter 30 -o Part1_impute

I do not understand why the MCMC iteration are not 30, but 1.
(see output)

----------------  Run parameters 
----------------

        reference haplotypes: 5008 [Panel 0]
           study individuals: 959 [Panel 2]
           sequence interval: [100000,5000000]
                      buffer: 250 kb
                          Ne: 2000
           input call thresh: 0.900
     burn-in MCMC iterations: 0
       total MCMC iterations: 1 (1 used for inference)    HMM states for imputation: 500 [Panel 0->2]
                active flags: <-use_prephased_g>

---------  Run log 
---------

RESETTING PARAMETERS FOR "SURROGATE FAMILY" MODELING
-setting mutation matrices
-setting switch rates

MCMC iteration [1/1]


impute2


mcmc

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