1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
|
+-----------------------------+
| |
| 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
|
