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DEploid-dev / DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
http://deploid.readthedocs.io/en/latest/index.html
GNU General Public License v3.0
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compute diagnostics #214

Closed shajoezhu closed 7 years ago

shajoezhu commented 7 years ago 
 MCMC step 100% completed.
##########################################
#        dEploid v0.3-release log        #
##########################################
Program was compiled on: Mon--8-May-08:15:25-UTC-2017
dEploid version: 8dad48b16b4a72c5bc3090aaacdac5eaa55d1be2

Input data: 
     Panel: labStrains.14.panel.txt
      PLAF: ../labStrains.14.PLAF.txt
       VCF: ../PG0389-C.14.vcf
   Exclude: exclude.14.txt

MCMC parameters: 
        MCMC burn: 0.5
      MCMC sample: 800
 MCMC sample rate: 5
      Random seed: 3
      Update Prop: YES
    Update Single: YES
      Update Pair: YES

Other parameters:
    Miss copy prob: 0.01
  Avrg Cent Morgan: 15000
                Ne: 10
     ScalingFactor: 100

MCMC diagnostic:
         Max_llks: -42186.9
  Mean_theta_llks: -41592.5
        Mean_llks: -41602.7
        Stdv_llks: 17.833
    DIC_by_Dtheta: 83225.6
      DIC_by_varD: 83841.4

Run time:
    Start at: Mon May  8 15:30:28 2017
      End at: Mon May  8 15:31:21 2017

Output saved to:
  Likelihood: PG0389-C.14.seed3.labStrains.llk
 Proportions: PG0389-C.14.seed3.labStrains.prop
  Haplotypes: PG0389-C.14.seed3.labStrains.hap

Proportions:
2.26302e-05 3.63182e-05   0.886311  0.000232506   0.113398
coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.1%) to 93.165% when pulling a26be24c4f8411f097f20a85f54ed1384666870d on issue213 into 8dad48b16b4a72c5bc3090aaacdac5eaa55d1be2 on master.

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.1%) to 93.165% when pulling a26be24c4f8411f097f20a85f54ed1384666870d on issue213 into 8dad48b16b4a72c5bc3090aaacdac5eaa55d1be2 on master.