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poruloh committed Nov 19, 2018
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66 changes: 33 additions & 33 deletions example/example.log
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Expand Up @@ -6,7 +6,7 @@
| |
+-----------------------------+

Copyright (C) 2015-2017 Harvard University.
Copyright (C) 2015-2018 Harvard University.
Distributed under the GNU GPLv3+ open source license.

Command line options:
Expand Down Expand Up @@ -56,25 +56,25 @@ Setting --histFactor=1.00

BEGINNING STEP 1

Time for step 1: 0.355483
Time for step 1 MN^2: 0.0182696
Time for step 1: 0.347481
Time for step 1 MN^2: 0.0270685

Making hard calls (time: 0.0182719)
Making hard calls (time: 0.0181408)


BEGINNING STEP 2

BATCH 1 OF 1
Building hash tables
.................................................................. (time: 0.064307)
.................................................................. (time: 0.065696)

Phasing samples 1-379
Time for phasing batch: 0.310312
Time for phasing batch: 0.309231

Making hard calls (time: 0.0180111)
Making hard calls (time: 0.0192151)

Time for step 2: 0.392636
Time for step 2 MN^2: 0.0401966
Time for step 2: 0.394149
Time for step 2 MN^2: 0.0408464


BEGINNING STEP 3 (PBWT ITERS)
Expand All @@ -87,108 +87,108 @@ BEGINNING PBWT ITER 1
BATCH 1 OF 10

Phasing samples 1-37
Time for phasing batch: 0.974292
Time for phasing batch: 0.977095

BATCH 2 OF 10

Phasing samples 38-75
Time for phasing batch: 0.908252
Time for phasing batch: 0.898498

BATCH 3 OF 10

Phasing samples 76-113
Time for phasing batch: 0.932394
Time for phasing batch: 0.950794

BATCH 4 OF 10

Phasing samples 114-151
Time for phasing batch: 0.931995
Time for phasing batch: 0.937661

BATCH 5 OF 10

Phasing samples 152-189
Time for phasing batch: 0.930893
Time for phasing batch: 0.909736

BATCH 6 OF 10

Phasing samples 190-227
Time for phasing batch: 0.92509
Time for phasing batch: 0.924443

BATCH 7 OF 10

Phasing samples 228-265
Time for phasing batch: 0.902272
Time for phasing batch: 0.9072

BATCH 8 OF 10

Phasing samples 266-303
Time for phasing batch: 0.874671
Time for phasing batch: 0.926957

BATCH 9 OF 10

Phasing samples 304-341
Time for phasing batch: 0.899732
Time for phasing batch: 0.888218

BATCH 10 OF 10

Phasing samples 342-379
Time for phasing batch: 0.92043
Time for phasing batch: 0.90299

Time for PBWT iter 1: 9.20008
Time for PBWT iter 1: 9.22363

BEGINNING PBWT ITER 2

BATCH 1 OF 10

Phasing samples 1-37
Time for phasing batch: 1.52217
Time for phasing batch: 1.49903

BATCH 2 OF 10

Phasing samples 38-75
Time for phasing batch: 1.48203
Time for phasing batch: 1.4698

BATCH 3 OF 10

Phasing samples 76-113
Time for phasing batch: 1.51264
Time for phasing batch: 1.51891

BATCH 4 OF 10

Phasing samples 114-151
Time for phasing batch: 1.44984
Time for phasing batch: 1.45062

BATCH 5 OF 10

Phasing samples 152-189
Time for phasing batch: 1.44166
Time for phasing batch: 1.42069

BATCH 6 OF 10

Phasing samples 190-227
Time for phasing batch: 1.48509
Time for phasing batch: 1.4851

BATCH 7 OF 10

Phasing samples 228-265
Time for phasing batch: 1.45803
Time for phasing batch: 1.44716

BATCH 8 OF 10

Phasing samples 266-303
Time for phasing batch: 1.42937
Time for phasing batch: 1.49382

BATCH 9 OF 10

Phasing samples 304-341
Time for phasing batch: 1.45571
Time for phasing batch: 1.43647

BATCH 10 OF 10

Phasing samples 342-379
Time for phasing batch: 1.43781
Time for phasing batch: 1.46241

Time for PBWT iter 2: 14.6745
Time for PBWT iter 2: 14.6841
Writing .haps.gz and .sample output
Time for writing output: 0.275763
Total elapsed time for analysis = 25.233 sec
Time for writing output: 0.221324
Total elapsed time for analysis = 24.9776 sec
10 changes: 5 additions & 5 deletions example/example_ref.log
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Expand Up @@ -6,7 +6,7 @@
| |
+-----------------------------+

Copyright (C) 2015-2017 Harvard University.
Copyright (C) 2015-2018 Harvard University.
Distributed under the GNU GPLv3+ open source license.

Command line options:
Expand Down Expand Up @@ -43,7 +43,7 @@ Average # SNPs per cM: 42
Number of <=(64-SNP, 1cM) segments: 9
Average # SNPs per segment: 47

Time for reading input: 5.09883 sec
Time for reading input: 5.09263 sec

Fraction of heterozygous genotypes: 0.178114
Typical span of default 100-het history length: 13.44 cM
Expand All @@ -59,15 +59,15 @@ PHASING ITER 1 OF 1

Phasing target samples
................................................................................
Time for phasing iter 1: 0.130578
Time for phasing iter 1: 0.132139
Writing vcf.gz output to target.phased.vcf.gz
[W::vcf_parse] INFO 'AC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AN' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AFR_AF' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'EX_TARGET' is not defined in the header, assuming Type=String
Time for writing output: 0.034054
Total elapsed time for analysis = 5.26409 sec
Time for writing output: 0.0356269
Total elapsed time for analysis = 5.26099 sec

Mean phase confidence of each target individual:
ID PHASE_CONFIDENCE
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66 changes: 33 additions & 33 deletions example/example_vcf.log
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Expand Up @@ -6,7 +6,7 @@
| |
+-----------------------------+

Copyright (C) 2015-2017 Harvard University.
Copyright (C) 2015-2018 Harvard University.
Distributed under the GNU GPLv3+ open source license.

Command line options:
Expand Down Expand Up @@ -39,25 +39,25 @@ Setting --histFactor=1.00

BEGINNING STEP 1

Time for step 1: 0.26742
Time for step 1 MN^2: 0.0206005
Time for step 1: 0.263286
Time for step 1 MN^2: 0.0227702

Making hard calls (time: 0.0133271)
Making hard calls (time: 0.018074)


BEGINNING STEP 2

BATCH 1 OF 1
Building hash tables
.................................................................. (time: 0.0492489)
.................................................................. (time: 0.0552511)

Phasing samples 1-379
Time for phasing batch: 0.294299
Time for phasing batch: 0.292423

Making hard calls (time: 0.014683)
Making hard calls (time: 0.0192568)

Time for step 2: 0.358237
Time for step 2 MN^2: 0.038358
Time for step 2: 0.366938
Time for step 2 MN^2: 0.0381578


BEGINNING STEP 3 (PBWT ITERS)
Expand All @@ -70,108 +70,108 @@ BEGINNING PBWT ITER 1
BATCH 1 OF 10

Phasing samples 1-37
Time for phasing batch: 1.03369
Time for phasing batch: 1.02615

BATCH 2 OF 10

Phasing samples 38-75
Time for phasing batch: 0.99218
Time for phasing batch: 0.964455

BATCH 3 OF 10

Phasing samples 76-113
Time for phasing batch: 0.998885
Time for phasing batch: 0.988999

BATCH 4 OF 10

Phasing samples 114-151
Time for phasing batch: 0.969435
Time for phasing batch: 0.978426

BATCH 5 OF 10

Phasing samples 152-189
Time for phasing batch: 0.932614
Time for phasing batch: 0.935981

BATCH 6 OF 10

Phasing samples 190-227
Time for phasing batch: 0.92777
Time for phasing batch: 0.941438

BATCH 7 OF 10

Phasing samples 228-265
Time for phasing batch: 0.930884
Time for phasing batch: 0.935864

BATCH 8 OF 10

Phasing samples 266-303
Time for phasing batch: 0.924231
Time for phasing batch: 0.926938

BATCH 9 OF 10

Phasing samples 304-341
Time for phasing batch: 0.941741
Time for phasing batch: 0.927558

BATCH 10 OF 10

Phasing samples 342-379
Time for phasing batch: 0.949201
Time for phasing batch: 0.932059

Time for PBWT iter 1: 9.60067
Time for PBWT iter 1: 9.55792

BEGINNING PBWT ITER 2

BATCH 1 OF 10

Phasing samples 1-37
Time for phasing batch: 1.54516
Time for phasing batch: 1.56033

BATCH 2 OF 10

Phasing samples 38-75
Time for phasing batch: 1.53539
Time for phasing batch: 1.49036

BATCH 3 OF 10

Phasing samples 76-113
Time for phasing batch: 1.57556
Time for phasing batch: 1.51976

BATCH 4 OF 10

Phasing samples 114-151
Time for phasing batch: 1.44469
Time for phasing batch: 1.48635

BATCH 5 OF 10

Phasing samples 152-189
Time for phasing batch: 1.43678
Time for phasing batch: 1.43754

BATCH 6 OF 10

Phasing samples 190-227
Time for phasing batch: 1.53198
Time for phasing batch: 1.50166

BATCH 7 OF 10

Phasing samples 228-265
Time for phasing batch: 1.53109
Time for phasing batch: 1.48078

BATCH 8 OF 10

Phasing samples 266-303
Time for phasing batch: 1.4952
Time for phasing batch: 1.45079

BATCH 9 OF 10

Phasing samples 304-341
Time for phasing batch: 1.50751
Time for phasing batch: 1.47995

BATCH 10 OF 10

Phasing samples 342-379
Time for phasing batch: 1.52464
Time for phasing batch: 1.42872

Time for PBWT iter 2: 15.128
Time for PBWT iter 2: 14.8363
Writing vcf.gz output to phased.vcf.gz
Time for writing output: 0.154516
Total elapsed time for analysis = 30.6983 sec
Time for writing output: 0.176335
Total elapsed time for analysis = 30.3964 sec
2 changes: 1 addition & 1 deletion src/EagleMain.cpp
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Expand Up @@ -215,7 +215,7 @@ int main(int argc, char *argv[]) {
cout << " +-----------------------------+" << endl;
cout << endl;

cout << "Copyright (C) 2015-2017 Harvard University." << endl;
cout << "Copyright (C) 2015-2018 Harvard University." << endl;
cout << "Distributed under the GNU GPLv3+ open source license." << endl << endl;

//cout << "Boost version: " << BOOST_LIB_VERSION << endl;
Expand Down

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