                      +-----------------------------+
                      |                             |
                      |   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 \
    --vcf=EUR_test.vcf.gz \
    --geneticMapFile=../tables/genetic_map_hg19_withX.txt.gz \
    --chrom=21 \
    --outPrefix=phased \
    --numThreads=4 

Setting number of threads to 4

=== Reading genotype data ===

Reading genotypes for N = 379 samples
Read M = 1813 variants
Filling in genetic map coordinates using reference file:
  ../tables/genetic_map_hg19_withX.txt.gz
Physical distance range: 9752235 base pairs
Genetic distance range:  23.0881 cM
Average # SNPs per cM:   79
Auto-selecting --maxBlockLen: 0.25 cM
Number of <=(64-SNP, 0.25cM) segments: 68
Average # SNPs per segment: 26
Estimating LD scores using 379 indivs
Fraction of heterozygous genotypes: 0.246308
Typical span of default 100-het history length: 5.17 cM
Setting --histFactor=1.00

BEGINNING STEP 1

Time for step 1: 0.263286
Time for step 1 MN^2: 0.0227702

Making hard calls (time: 0.018074)


BEGINNING STEP 2

BATCH 1 OF 1
Building hash tables
.................................................................. (time: 0.0552511)

Phasing samples 1-379
Time for phasing batch: 0.292423

Making hard calls (time: 0.0192568)

Time for step 2: 0.366938
Time for step 2 MN^2: 0.0381578


BEGINNING STEP 3 (PBWT ITERS)

Auto-selecting number of PBWT iterations: setting --pbwtIters to 2


BEGINNING PBWT ITER 1

BATCH 1 OF 10

Phasing samples 1-37
Time for phasing batch: 1.02615

BATCH 2 OF 10

Phasing samples 38-75
Time for phasing batch: 0.964455

BATCH 3 OF 10

Phasing samples 76-113
Time for phasing batch: 0.988999

BATCH 4 OF 10

Phasing samples 114-151
Time for phasing batch: 0.978426

BATCH 5 OF 10

Phasing samples 152-189
Time for phasing batch: 0.935981

BATCH 6 OF 10

Phasing samples 190-227
Time for phasing batch: 0.941438

BATCH 7 OF 10

Phasing samples 228-265
Time for phasing batch: 0.935864

BATCH 8 OF 10

Phasing samples 266-303
Time for phasing batch: 0.926938

BATCH 9 OF 10

Phasing samples 304-341
Time for phasing batch: 0.927558

BATCH 10 OF 10

Phasing samples 342-379
Time for phasing batch: 0.932059

Time for PBWT iter 1: 9.55792

BEGINNING PBWT ITER 2

BATCH 1 OF 10

Phasing samples 1-37
Time for phasing batch: 1.56033

BATCH 2 OF 10

Phasing samples 38-75
Time for phasing batch: 1.49036

BATCH 3 OF 10

Phasing samples 76-113
Time for phasing batch: 1.51976

BATCH 4 OF 10

Phasing samples 114-151
Time for phasing batch: 1.48635

BATCH 5 OF 10

Phasing samples 152-189
Time for phasing batch: 1.43754

BATCH 6 OF 10

Phasing samples 190-227
Time for phasing batch: 1.50166

BATCH 7 OF 10

Phasing samples 228-265
Time for phasing batch: 1.48078

BATCH 8 OF 10

Phasing samples 266-303
Time for phasing batch: 1.45079

BATCH 9 OF 10

Phasing samples 304-341
Time for phasing batch: 1.47995

BATCH 10 OF 10

Phasing samples 342-379
Time for phasing batch: 1.42872

Time for PBWT iter 2: 14.8363
Writing vcf.gz output to phased.vcf.gz
Time for writing output: 0.176335
Total elapsed time for analysis = 30.3964 sec
