                      +-----------------------------+
                      |                             |
                      |   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 \
    --bfile=EUR_test \
    --geneticMapFile=USE_BIM \
    --chrom=21 \
    --outPrefix=phased \
    --numThreads=4 

Setting number of threads to 4

=== Reading genotype data ===

Reading fam file: EUR_test.fam
Total indivs in PLINK data: Nbed = 379
Total indivs stored in memory: NpreQC = 379
Reading bim file: EUR_test.bim
Total snps in PLINK data: Mbed = 2000
Restricting to 1813 SNPs on chrom 21 in region [bpStart,bpEnd] = [0,1e+09]
Total SNPs stored in memory: MpreQC = 1813
Allocating 1813 x 379 bytes to temporarily store genotypes
Reading genotypes and performing QC filtering on snps and indivs...
Reading bed file: EUR_test.bed
    Expecting 190000 (+3) bytes for 379 indivs, 2000 snps

Total post-QC indivs: N = 379
Total post-QC SNPs: M = 1813
MAF spectrum: 
     0- 5%:     495
     5-10%:     290
    10-20%:     332
    20-30%:     248
    30-40%:     234
    40-50%:     214
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: 0.347481
Time for step 1 MN^2: 0.0270685

Making hard calls (time: 0.0181408)


BEGINNING STEP 2

BATCH 1 OF 1
Building hash tables
.................................................................. (time: 0.065696)

Phasing samples 1-379
Time for phasing batch: 0.309231

Making hard calls (time: 0.0192151)

Time for step 2: 0.394149
Time for step 2 MN^2: 0.0408464


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: 0.977095

BATCH 2 OF 10

Phasing samples 38-75
Time for phasing batch: 0.898498

BATCH 3 OF 10

Phasing samples 76-113
Time for phasing batch: 0.950794

BATCH 4 OF 10

Phasing samples 114-151
Time for phasing batch: 0.937661

BATCH 5 OF 10

Phasing samples 152-189
Time for phasing batch: 0.909736

BATCH 6 OF 10

Phasing samples 190-227
Time for phasing batch: 0.924443

BATCH 7 OF 10

Phasing samples 228-265
Time for phasing batch: 0.9072

BATCH 8 OF 10

Phasing samples 266-303
Time for phasing batch: 0.926957

BATCH 9 OF 10

Phasing samples 304-341
Time for phasing batch: 0.888218

BATCH 10 OF 10

Phasing samples 342-379
Time for phasing batch: 0.90299

Time for PBWT iter 1: 9.22363

BEGINNING PBWT ITER 2

BATCH 1 OF 10

Phasing samples 1-37
Time for phasing batch: 1.49903

BATCH 2 OF 10

Phasing samples 38-75
Time for phasing batch: 1.4698

BATCH 3 OF 10

Phasing samples 76-113
Time for phasing batch: 1.51891

BATCH 4 OF 10

Phasing samples 114-151
Time for phasing batch: 1.45062

BATCH 5 OF 10

Phasing samples 152-189
Time for phasing batch: 1.42069

BATCH 6 OF 10

Phasing samples 190-227
Time for phasing batch: 1.4851

BATCH 7 OF 10

Phasing samples 228-265
Time for phasing batch: 1.44716

BATCH 8 OF 10

Phasing samples 266-303
Time for phasing batch: 1.49382

BATCH 9 OF 10

Phasing samples 304-341
Time for phasing batch: 1.43647

BATCH 10 OF 10

Phasing samples 342-379
Time for phasing batch: 1.46241

Time for PBWT iter 2: 14.6841
Writing .haps.gz and .sample output
Time for writing output: 0.221324
Total elapsed time for analysis = 24.9776 sec
