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
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
|
+-----------------------------+
| |
| 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
|
