                      +-----------------------------+
                      |                             |
                      |   Eagle v2.4.1              |
                      |   November 18, 2018         |
                      |   Po-Ru Loh                 |
                      |                             |
                      +-----------------------------+

Copyright (C) 2015-2018 Harvard University.
Distributed under the GNU GPLv3+ open source license.

Command line options:

../eagle \
    --vcfRef=ref.bcf \
    --vcfTarget=target.vcf.gz \
    --geneticMapFile=../tables/genetic_map_hg19_withX.txt.gz \
    --outPrefix=target.phased 

Setting number of threads to 1
[W::hts_idx_load2] The index file is older than the data file: ref.bcf.csi

Reference samples: Nref = 169
Target samples: Ntarget = 8
[W::vcf_parse] INFO 'AC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AN' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AFR_AF' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'EX_TARGET' is not defined in the header, assuming Type=String
SNPs to analyze: M = 430 SNPs in both target and reference

SNPs ignored: 0 SNPs in target but not reference
              215 SNPs in reference but not target
              0 multi-allelic SNPs in target

Missing rate in target genotypes: 0.00116279

Filling in genetic map coordinates using reference file:
  ../tables/genetic_map_hg19_withX.txt.gz
Physical distance range: 3595565 base pairs
Genetic distance range:  10.292 cM
Average # SNPs per cM:   42
Number of <=(64-SNP, 1cM) segments: 9
Average # SNPs per segment: 47

Time for reading input: 5.09263 sec

Fraction of heterozygous genotypes: 0.178114
Typical span of default 100-het history length: 13.44 cM
Setting --histFactor=1.00

Auto-selecting number of phasing iterations: setting --pbwtIters to 1


BEGINNING PHASING

PHASING ITER 1 OF 1


Phasing target samples
................................................................................
Time for phasing iter 1: 0.132139
Writing vcf.gz output to target.phased.vcf.gz
[W::vcf_parse] INFO 'AC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AN' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AFR_AF' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'EX_TARGET' is not defined in the header, assuming Type=String
Time for writing output: 0.0356269
Total elapsed time for analysis = 5.26099 sec

Mean phase confidence of each target individual:
ID	PHASE_CONFIDENCE
HG00403	0.953163
HG00404	0.949485
HG00406	0.927005
HG00407	0.950292
HG00419	0.938822
HG00421	0.93367
HG00422	0.952224
HG00428	0.944651
