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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 \
--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: 0.373152
Time for step 1 MN^2: 0.0242926
Making hard calls (time: 0.0283859)
BEGINNING STEP 2
BATCH 1 OF 1
Building hash tables
.................................................................. (time: 0.0523882)
Phasing samples 1-379
Time for phasing batch: 0.449098
Making hard calls (time: 0.029567)
Time for step 2: 0.531062
Time for step 2 MN^2: 0.0591508
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: 1.75458
BATCH 2 OF 10
Phasing samples 38-75
Time for phasing batch: 1.59901
BATCH 3 OF 10
Phasing samples 76-113
Time for phasing batch: 1.69437
BATCH 4 OF 10
Phasing samples 114-151
Time for phasing batch: 1.62289
BATCH 5 OF 10
Phasing samples 152-189
Time for phasing batch: 1.59901
BATCH 6 OF 10
Phasing samples 190-227
Time for phasing batch: 1.63321
BATCH 7 OF 10
Phasing samples 228-265
Time for phasing batch: 1.63894
BATCH 8 OF 10
Phasing samples 266-303
Time for phasing batch: 1.57722
BATCH 9 OF 10
Phasing samples 304-341
Time for phasing batch: 1.56258
BATCH 10 OF 10
Phasing samples 342-379
Time for phasing batch: 1.63269
Time for PBWT iter 1: 16.3145
BEGINNING PBWT ITER 2
BATCH 1 OF 10
Phasing samples 1-37
Time for phasing batch: 2.73515
BATCH 2 OF 10
Phasing samples 38-75
Time for phasing batch: 2.58695
BATCH 3 OF 10
Phasing samples 76-113
Time for phasing batch: 2.70714
BATCH 4 OF 10
Phasing samples 114-151
Time for phasing batch: 2.54992
BATCH 5 OF 10
Phasing samples 152-189
Time for phasing batch: 2.51631
BATCH 6 OF 10
Phasing samples 190-227
Time for phasing batch: 2.62562
BATCH 7 OF 10
Phasing samples 228-265
Time for phasing batch: 2.60083
BATCH 8 OF 10
Phasing samples 266-303
Time for phasing batch: 2.4503
BATCH 9 OF 10
Phasing samples 304-341
Time for phasing batch: 2.54366
BATCH 10 OF 10
Phasing samples 342-379
Time for phasing batch: 2.56976
Time for PBWT iter 2: 25.8857
Writing .haps.gz and .sample output
Time for writing output: 0.370972
Total elapsed time for analysis = 43.6733 sec
|
