bio-eagle-examples 2.4-1 / usr / share / doc / bio-eagle / examples / example.log

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                      +-----------------------------+
                      |                             |
                      |   Eagle v2.4                |
                      |   December 13, 2017         |
                      |   Po-Ru Loh                 |
                      |                             |
                      +-----------------------------+

Copyright (C) 2015-2017 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: 0.282519
Time for step 1 MN^2: 0.0201082

Making hard calls (time: 0.0164621)


BEGINNING STEP 2

BATCH 1 OF 1
Building hash tables
.................................................................. (time: 0.0826769)

Phasing samples 1-379
Time for phasing batch: 0.335781

Making hard calls (time: 0.0172811)

Time for step 2: 0.435747
Time for step 2 MN^2: 0.0391194


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: 1.13401

BATCH 2 OF 10

Phasing samples 38-75
Time for phasing batch: 1.04853

BATCH 3 OF 10

Phasing samples 76-113
Time for phasing batch: 1.18956

BATCH 4 OF 10

Phasing samples 114-151
Time for phasing batch: 1.1353

BATCH 5 OF 10

Phasing samples 152-189
Time for phasing batch: 1.01419

BATCH 6 OF 10

Phasing samples 190-227
Time for phasing batch: 1.05172

BATCH 7 OF 10

Phasing samples 228-265
Time for phasing batch: 0.99322

BATCH 8 OF 10

Phasing samples 266-303
Time for phasing batch: 0.99847

BATCH 9 OF 10

Phasing samples 304-341
Time for phasing batch: 0.998471

BATCH 10 OF 10

Phasing samples 342-379
Time for phasing batch: 1.05052

Time for PBWT iter 1: 10.6142

BEGINNING PBWT ITER 2

BATCH 1 OF 10

Phasing samples 1-37
Time for phasing batch: 1.76314

BATCH 2 OF 10

Phasing samples 38-75
Time for phasing batch: 1.79145

BATCH 3 OF 10

Phasing samples 76-113
Time for phasing batch: 1.8253

BATCH 4 OF 10

Phasing samples 114-151
Time for phasing batch: 1.54563

BATCH 5 OF 10

Phasing samples 152-189
Time for phasing batch: 1.54299

BATCH 6 OF 10

Phasing samples 190-227
Time for phasing batch: 1.59936

BATCH 7 OF 10

Phasing samples 228-265
Time for phasing batch: 1.55847

BATCH 8 OF 10

Phasing samples 266-303
Time for phasing batch: 1.51538

BATCH 9 OF 10

Phasing samples 304-341
Time for phasing batch: 1.58919

BATCH 10 OF 10

Phasing samples 342-379
Time for phasing batch: 1.64308

Time for PBWT iter 2: 16.3741
Writing .haps.gz and .sample output
Time for writing output: 0.281509
Total elapsed time for analysis = 28.1508 sec

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