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|
+-----------------------------+
| |
| Eagle v2.3 |
| July 22, 2016 |
| Po-Ru Loh |
| |
+-----------------------------+
Copyright (C) 2015-2016 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: 0.375713
Time for step 1 MN^2: 0.0244864
Making hard calls (time: 0.028863)
BEGINNING STEP 2
BATCH 1 OF 1
Building hash tables
.................................................................. (time: 0.0508139)
Phasing samples 1-379
Time for phasing batch: 0.437996
Making hard calls (time: 0.029588)
Time for step 2: 0.51841
Time for step 2 MN^2: 0.0594165
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: 1.77567
BATCH 2 OF 10
Phasing samples 38-75
Time for phasing batch: 1.64262
BATCH 3 OF 10
Phasing samples 76-113
Time for phasing batch: 1.71332
BATCH 4 OF 10
Phasing samples 114-151
Time for phasing batch: 1.61786
BATCH 5 OF 10
Phasing samples 152-189
Time for phasing batch: 1.6091
BATCH 6 OF 10
Phasing samples 190-227
Time for phasing batch: 1.6461
BATCH 7 OF 10
Phasing samples 228-265
Time for phasing batch: 1.651
BATCH 8 OF 10
Phasing samples 266-303
Time for phasing batch: 1.58484
BATCH 9 OF 10
Phasing samples 304-341
Time for phasing batch: 1.59481
BATCH 10 OF 10
Phasing samples 342-379
Time for phasing batch: 1.63671
Time for PBWT iter 1: 16.4721
BEGINNING PBWT ITER 2
BATCH 1 OF 10
Phasing samples 1-37
Time for phasing batch: 2.72875
BATCH 2 OF 10
Phasing samples 38-75
Time for phasing batch: 2.59217
BATCH 3 OF 10
Phasing samples 76-113
Time for phasing batch: 2.72183
BATCH 4 OF 10
Phasing samples 114-151
Time for phasing batch: 2.57471
BATCH 5 OF 10
Phasing samples 152-189
Time for phasing batch: 2.5283
BATCH 6 OF 10
Phasing samples 190-227
Time for phasing batch: 2.64632
BATCH 7 OF 10
Phasing samples 228-265
Time for phasing batch: 2.63781
BATCH 8 OF 10
Phasing samples 266-303
Time for phasing batch: 2.52006
BATCH 9 OF 10
Phasing samples 304-341
Time for phasing batch: 2.53771
BATCH 10 OF 10
Phasing samples 342-379
Time for phasing batch: 2.51691
Time for PBWT iter 2: 26.0046
Writing vcf.gz output to phased.vcf.gz
Time for writing output: 0.331217
Total elapsed time for analysis = 52.9965 sec
|
