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SNPRelate.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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> BiocGenerics:::testPackage("SNPRelate")
SNPRelate
Genetic Relationship Matrix (GRM, GCTA):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 1,000 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities:
Sat Apr 13 05:41:31 2019 (internal increment: 11612)
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Saving to the GDS file:
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Sat Apr 13 05:41:32 2019 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 2,000 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities:
Sat Apr 13 05:41:32 2019 (internal increment: 11612)
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Saving to the GDS file:
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Sat Apr 13 05:41:33 2019 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 3,800 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities:
Sat Apr 13 05:41:33 2019 (internal increment: 11612)
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Saving to the GDS file:
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Sat Apr 13 05:41:34 2019 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
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Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 6,800 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities:
Sat Apr 13 05:41:35 2019 (internal increment: 11612)
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Sat Apr 13 05:41:36 2019 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 1,000 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities:
Sat Apr 13 05:41:36 2019 (internal increment: 65536)
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Saving to the GDS file:
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Sat Apr 13 05:41:37 2019 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 2,000 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities:
Sat Apr 13 05:41:37 2019 (internal increment: 65536)
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Saving to the GDS file:
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Sat Apr 13 05:41:39 2019 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 3,800 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities:
Sat Apr 13 05:41:39 2019 (internal increment: 65536)
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Saving to the GDS file:
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Sat Apr 13 05:41:40 2019 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
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Writing ...
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Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 6,800 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities:
Sat Apr 13 05:41:41 2019 (internal increment: 65536)
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Sat Apr 13 05:41:42 2019 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 279 samples, 1000 SNPs
using 1 (CPU) core.
method: covariance
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 279 samples, 1000 SNPs
using 1 (CPU) core.
method: correlation
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
FUNCTION: SNPGDSFileClass
FUNCTION: SNPRelate-package
Start snpgdsBED2GDS ...
BED file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz" in the SNP-major mode (Sample X SNP)
FAM file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz", DONE.
BIM file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz", DONE.
Sat Apr 13 05:41:46 2019 store sample id, snp id, position, and chromosome.
start writing: 60 samples, 5000 SNPs ...
Sat Apr 13 05:41:46 2019 0%
Sat Apr 13 05:41:46 2019 100%
Sat Apr 13 05:41:46 2019 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
Principal Component Analysis (PCA) on genotypes:
Excluding 203 SNPs on non-autosomes
Excluding 28 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 60 samples, 4,769 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 124273
CPU capabilities:
Sat Apr 13 05:41:46 2019 (internal increment: 53996)
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Sat Apr 13 05:41:47 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:41:47 2019 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
PLINK IBD: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:41:47 2019 (internal increment: 65536)
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Sat Apr 13 05:41:48 2019 Done.
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:41:49 2019 (internal increment: 65536)
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Sat Apr 13 05:41:50 2019 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 279 samples, 200 SNPs
using 1 (CPU) core.
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 55417
FUNCTION: hapmap_geno
FUNCTION: snpgdsAdmixPlot
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities:
Sat Apr 13 05:41:51 2019 (internal increment: 11612)
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Sat Apr 13 05:41:51 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:41:51 2019 Done.
FUNCTION: snpgdsAdmixProp
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities:
Sat Apr 13 05:41:52 2019 (internal increment: 11612)
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Sat Apr 13 05:41:52 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:41:52 2019 Done.
FUNCTION: snpgdsAlleleSwitch
Strand-switching at 50 SNP locus/loci.
Unable to determine switching at 10 SNP locus/loci.
FUNCTION: snpgdsApartSelection
Sat Apr 13 05:41:53 2019 Chromosome 1, # of SNPs: 365
Sat Apr 13 05:41:53 2019 Chromosome 2, # of SNPs: 370
Sat Apr 13 05:41:53 2019 Chromosome 3, # of SNPs: 314
Sat Apr 13 05:41:53 2019 Chromosome 4, # of SNPs: 294
Sat Apr 13 05:41:53 2019 Chromosome 5, # of SNPs: 291
Sat Apr 13 05:41:53 2019 Chromosome 6, # of SNPs: 280
Sat Apr 13 05:41:53 2019 Chromosome 7, # of SNPs: 245
Sat Apr 13 05:41:53 2019 Chromosome 8, # of SNPs: 232
Sat Apr 13 05:41:53 2019 Chromosome 9, # of SNPs: 203
Sat Apr 13 05:41:53 2019 Chromosome 10, # of SNPs: 224
Sat Apr 13 05:41:53 2019 Chromosome 11, # of SNPs: 227
Sat Apr 13 05:41:53 2019 Chromosome 12, # of SNPs: 215
Sat Apr 13 05:41:53 2019 Chromosome 13, # of SNPs: 175
Sat Apr 13 05:41:53 2019 Chromosome 14, # of SNPs: 147
Sat Apr 13 05:41:53 2019 Chromosome 15, # of SNPs: 127
Sat Apr 13 05:41:53 2019 Chromosome 16, # of SNPs: 128
Sat Apr 13 05:41:53 2019 Chromosome 17, # of SNPs: 112
Sat Apr 13 05:41:53 2019 Chromosome 18, # of SNPs: 127
Sat Apr 13 05:41:53 2019 Chromosome 19, # of SNPs: 76
Sat Apr 13 05:41:53 2019 Chromosome 20, # of SNPs: 107
Sat Apr 13 05:41:53 2019 Chromosome 21, # of SNPs: 63
Sat Apr 13 05:41:53 2019 Chromosome 22, # of SNPs: 54
Sat Apr 13 05:41:53 2019 Chromosome 23, # of SNPs: 215
Total # of SNPs selected:4591
FUNCTION: snpgdsBED2GDS
Start snpgdsBED2GDS ...
BED file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz" in the SNP-major mode (Sample X SNP)
FAM file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz", DONE.
BIM file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz", DONE.
Sat Apr 13 05:41:53 2019 store sample id, snp id, position, and chromosome.
start writing: 60 samples, 5000 SNPs ...
Sat Apr 13 05:41:53 2019 0%
Sat Apr 13 05:41:53 2019 100%
Sat Apr 13 05:41:53 2019 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
FUNCTION: snpgdsClose
FUNCTION: snpgdsCombineGeno
Create a GDS genotype file:
The new dataset consists of 10 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 20 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
10 samples, 3000 SNPs
open 't2.gds' ...
20 samples, 3000 SNPs
Concatenating samples (mapping to the first GDS file) ...
reference: 3000 SNPs (100.0%)
file 2: 0 allele flips, 0 ambiguous locus/loci
[no flip]: 3000
create 'test.gds': 30 samples, 3000 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (46.2K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (46.0K, reduced: 204B)
# of fragments: 15
Done.
Create a GDS genotype file:
The new dataset consists of 279 samples and 100 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 279 samples and 200 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
279 samples, 100 SNPs
open 't2.gds' ...
279 samples, 200 SNPs
Concatenating SNPs ...
create 'test.gds': 279 samples, 300 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (19.1K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (18.9K, reduced: 204B)
# of fragments: 15
Done.
FUNCTION: snpgdsCreateGeno
Principal Component Analysis (PCA) on genotypes:
Excluding 42 SNPs on non-autosomes
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 958 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 264760
CPU capabilities:
Sat Apr 13 05:41:53 2019 (internal increment: 11612)
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Sat Apr 13 05:41:54 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:41:54 2019 Done.
FUNCTION: snpgdsCreateGenoSet
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 75.42%, 540/716
Chromosome 2: 72.24%, 536/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.31%, 412/562
Chromosome 5: 77.03%, 436/566
Chromosome 6: 75.58%, 427/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.31%, 348/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.33%, 359/483
Chromosome 11: 77.40%, 346/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 75.58%, 260/344
Chromosome 14: 76.95%, 217/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 74.40%, 154/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,547 markers are selected in total.
Create a GDS genotype file:
The new dataset consists of 279 samples and 6547 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsCutTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Apr 13 05:41:54 2019 0%
Dissimilarity: Sat Apr 13 05:41:56 2019 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
Create 4 groups.
FUNCTION: snpgdsDiss
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Apr 13 05:41:57 2019 0%
Dissimilarity: Sat Apr 13 05:41:58 2019 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsDrawTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Apr 13 05:41:59 2019 0%
Dissimilarity: Sat Apr 13 05:42:01 2019 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsEIGMIX
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities:
Sat Apr 13 05:42:01 2019 (internal increment: 11612)
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Sat Apr 13 05:42:02 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:42:02 2019 Done.
FUNCTION: snpgdsErrMsg
FUNCTION: snpgdsExampleFileName
FUNCTION: snpgdsFst
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
Method: Weir & Cockerham, 1984
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
Method: Weir & Hill, 2002
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
FUNCTION: snpgdsGDS2BED
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to PLINK binary PED:
Working space: 279 samples, 8722 SNPs
Output a BIM file.
Output a BED file ...
Sat Apr 13 05:42:03 2019 0%
Sat Apr 13 05:42:03 2019 100%
Done.
FUNCTION: snpgdsGDS2Eigen
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to EIGENSOFT:
save to *.snp: 8722 snps
save to *.ind: 279 samples
Output: Sat Apr 13 05:42:03 2019 0%
Output: Sat Apr 13 05:42:03 2019 100%
Done.
FUNCTION: snpgdsGDS2PED
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Sat Apr 13 05:42:03 2019 0%
Output: Sat Apr 13 05:42:04 2019 100%
FUNCTION: snpgdsGEN2GDS
running snpgdsGEN2GDS ...
FUNCTION: snpgdsGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities:
Sat Apr 13 05:42:04 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:05 2019 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities:
Sat Apr 13 05:42:05 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:06 2019 Done.
FUNCTION: snpgdsGetGeno
Genotype matrix: 1000 SNPs X 279 samples
Genotype matrix: 279 samples X 1000 SNPs
FUNCTION: snpgdsHCluster
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Apr 13 05:42:06 2019 0%
Dissimilarity: Sat Apr 13 05:42:08 2019 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsHWE
Keeping 716 SNPs according to chromosome 1
Excluding 160 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
FUNCTION: snpgdsIBDKING
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities:
Sat Apr 13 05:42:09 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:09 2019 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities:
Sat Apr 13 05:42:09 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:10 2019 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
# of families: 20, and within- and between-family relationship are estimated differently.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities:
Sat Apr 13 05:42:11 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:11 2019 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Apr 13 05:42:11 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:12 2019 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Apr 13 05:42:12 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:12 2019 Done.
FUNCTION: snpgdsIBDMLE
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
Working space: 30 samples, 7,142 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.45%, 404/742
Chromosome 3: 55.67%, 339/609
Chromosome 4: 56.94%, 320/562
Chromosome 5: 56.71%, 321/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 55.72%, 263/472
Chromosome 8: 50.41%, 246/488
Chromosome 9: 54.33%, 226/416
Chromosome 10: 50.10%, 242/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 55.27%, 236/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 55.67%, 157/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 52.84%, 121/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 50.86%, 59/116
4,755 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 30 samples, 250 SNPs
using 1 (CPU) core
MLE IBD: the sum of all selected genotypes (0,1,2) = 7222
MLE IBD: Sat Apr 13 05:42:12 2019 0%
MLE IBD: Sat Apr 13 05:42:14 2019 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.482, sd: 0.283
MLE IBD: the sum of all selected genotypes (0,1,2) = 6018
MLE IBD: Sat Apr 13 05:42:14 2019 0%
MLE IBD: Sat Apr 13 05:42:14 2019 100%
FUNCTION: snpgdsIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
Working space: 30 samples, 7,142 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.45%, 404/742
Chromosome 3: 55.67%, 339/609
Chromosome 4: 56.94%, 320/562
Chromosome 5: 56.71%, 321/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 55.72%, 263/472
Chromosome 8: 50.41%, 246/488
Chromosome 9: 54.33%, 226/416
Chromosome 10: 50.10%, 242/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 55.27%, 236/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 55.67%, 157/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 52.84%, 121/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 50.86%, 59/116
4,755 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 30 samples, 250 SNPs
using 1 (CPU) core
MLE IBD: the sum of all selected genotypes (0,1,2) = 7222
MLE IBD: Sat Apr 13 05:42:14 2019 0%
MLE IBD: Sat Apr 13 05:42:15 2019 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.482, sd: 0.283
MLE IBD: the sum of all selected genotypes (0,1,2) = 6018
MLE IBD: Sat Apr 13 05:42:15 2019 0%
MLE IBD: Sat Apr 13 05:42:15 2019 100%
FUNCTION: snpgdsIBDMoM
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
PLINK IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Apr 13 05:42:15 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:16 2019 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 93 samples, 8,160 SNPs
using 1 (CPU) core
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Apr 13 05:42:16 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:16 2019 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 93 samples, 8,160 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Apr 13 05:42:16 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:16 2019 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 8,160 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 203285
Sat Apr 13 05:42:16 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:16 2019 Done.
FUNCTION: snpgdsIBDSelection
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 93 samples, 8,160 SNPs
using 1 (CPU) core
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Apr 13 05:42:16 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:16 2019 Done.
FUNCTION: snpgdsIBS
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:42:16 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 2s
Sat Apr 13 05:42:18 2019 Done.
FUNCTION: snpgdsIBSNum
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:42:18 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:19 2019 Done.
FUNCTION: snpgdsIndInb
Estimating individual inbreeding coefficients:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
FUNCTION: snpgdsIndInbCoef
FUNCTION: snpgdsIndivBeta
Individual Inbreeding and Relatedness (beta estimator):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Individual Beta: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities:
Sat Apr 13 05:42:20 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:21 2019 Done.
FUNCTION: snpgdsLDMat
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 279 samples, 203 SNPs
using 1 (CPU) core.
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 279 samples, 203 SNPs
using 1 (CPU) core.
sliding window size: 203
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
FUNCTION: snpgdsLDpair
FUNCTION: snpgdsLDpruning
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 75.42%, 540/716
Chromosome 2: 72.24%, 536/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.31%, 412/562
Chromosome 5: 77.03%, 436/566
Chromosome 6: 75.58%, 427/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.31%, 348/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.33%, 359/483
Chromosome 11: 77.40%, 346/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 75.58%, 260/344
Chromosome 14: 76.95%, 217/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 74.40%, 154/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,547 markers are selected in total.
FUNCTION: snpgdsMergeGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 6,800 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities:
Sat Apr 13 05:42:22 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:22 2019 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 3,400 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 951558
CPU capabilities:
Sat Apr 13 05:42:22 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:23 2019 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 3,400 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 957408
CPU capabilities:
Sat Apr 13 05:42:23 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:24 2019 Done.
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
FUNCTION: snpgdsOpen
FUNCTION: snpgdsOption
FUNCTION: snpgdsPCA
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities:
Sat Apr 13 05:42:25 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:26 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:42:26 2019 Done.
FUNCTION: snpgdsPCACorr
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities:
Sat Apr 13 05:42:26 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:26 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:42:27 2019 Done.
SNP Correlation:
Working space: 279 samples, 9088 SNPs
using 1 (CPU) core
using the top 4 eigenvectors
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Sat Apr 13 05:42:27 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:27 2019 Done.
SNP Correlation:
Working space: 279 samples, 9088 SNPs
using 1 (CPU) core
using the top 4 eigenvectors
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Sat Apr 13 05:42:27 2019
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:27 2019 Done.
FUNCTION: snpgdsPCASNPLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities:
Sat Apr 13 05:42:27 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:27 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:42:27 2019 Done.
SNP loading:
Working space: 279 samples, 8722 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:42:27 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:27 2019 Done.
FUNCTION: snpgdsPCASampLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities:
Sat Apr 13 05:42:28 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:28 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:42:28 2019 Done.
SNP loading:
Working space: 279 samples, 8722 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:42:28 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:28 2019 Done.
Sample loading:
Working space: 100 samples, 8722 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 878146
Sat Apr 13 05:42:28 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:28 2019 Done.
FUNCTION: snpgdsPED2GDS
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Sat Apr 13 05:42:28 2019 0%
Output: Sat Apr 13 05:42:29 2019 100%
PLINK PED/MAP to GDS Format:
Import 9088 variants from 'tmp.map'
Chromosome:
1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7
716 483 447 427 344 282 262 278 207 266 120 742 229 126 116 609 562 566 565 472
8 9 X
488 416 365
Reading 'tmp.ped'
Output: 'test.gds'
Import 279 samples
Transpose the genotypic matrix ...
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 50
save to 'test.gds.tmp'
rename 'test.gds.tmp' (711.4K, reduced: 618.7K)
# of fragments: 26
FUNCTION: snpgdsPairIBD
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
Working space: 93 samples, 7,077 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.40%, 463/742
Chromosome 3: 60.76%, 370/609
Chromosome 4: 64.59%, 363/562
Chromosome 5: 62.54%, 354/566
Chromosome 6: 60.00%, 339/565
Chromosome 7: 62.71%, 296/472
Chromosome 8: 58.61%, 286/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.66%, 293/483
Chromosome 11: 62.86%, 281/447
Chromosome 12: 63.00%, 269/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.48%, 179/282
Chromosome 15: 63.36%, 166/262
Chromosome 16: 61.87%, 172/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.02%, 157/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 67.25%, 154/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,429 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.506, sd: 0.300
MLE IBD: the sum of all selected genotypes (0,1,2) = 6339
MLE IBD: Sat Apr 13 05:42:30 2019 0%
MLE IBD: Sat Apr 13 05:42:31 2019 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.506, sd: 0.300
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6339
Sat Apr 13 05:42:31 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:31 2019 Done.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.506, sd: 0.300
MLE IBD: the sum of all selected genotypes (0,1,2) = 6339
MLE IBD: Sat Apr 13 05:42:31 2019 0%
MLE IBD: Sat Apr 13 05:42:31 2019 100%
Genotype matrix: 250 SNPs X 25 samples
[1] -364.4667
[1] -377.9771
[1] -390.3299
[1] -380.5342
[1] -378.2092
[1] -383.641
[1] -364.5406
[1] -375.196
[1] -383.5752
[1] -385.7771
[1] -368.6237
[1] -390.7766
[1] -367.5082
[1] -383.595
[1] -385.7602
[1] -378.5134
[1] -388.3292
[1] -376.4419
[1] -378.3509
[1] -386.8318
[1] -385.3803
[1] -382.988
[1] -369.9328
[1] -383.3912
FUNCTION: snpgdsPairIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
Working space: 93 samples, 7,077 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.40%, 463/742
Chromosome 3: 60.76%, 370/609
Chromosome 4: 64.59%, 363/562
Chromosome 5: 62.54%, 354/566
Chromosome 6: 60.00%, 339/565
Chromosome 7: 62.71%, 296/472
Chromosome 8: 58.61%, 286/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.66%, 293/483
Chromosome 11: 62.86%, 281/447
Chromosome 12: 63.00%, 269/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.48%, 179/282
Chromosome 15: 63.36%, 166/262
Chromosome 16: 61.87%, 172/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.02%, 157/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 67.25%, 154/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,429 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.506, sd: 0.300
MLE IBD: the sum of all selected genotypes (0,1,2) = 6339
MLE IBD: Sat Apr 13 05:42:32 2019 0%
MLE IBD: Sat Apr 13 05:42:33 2019 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.506, sd: 0.300
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6339
Sat Apr 13 05:42:33 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:33 2019 Done.
Genotype matrix: 250 SNPs X 25 samples
[1] -364.4667
[1] -377.9771
[1] -390.3299
[1] -380.5342
[1] -378.2092
[1] -383.641
[1] -364.5406
[1] -375.196
[1] -383.5752
[1] -385.7771
[1] -368.6237
[1] -390.7766
[1] -367.5082
[1] -383.595
[1] -385.7602
[1] -378.5134
[1] -388.3292
[1] -376.4419
[1] -378.3509
[1] -386.8318
[1] -385.3803
[1] -382.988
[1] -369.9328
[1] -383.3912
FUNCTION: snpgdsPairScore
Excluding 365 SNPs on non-autosomes
Working space: 120 samples, 8723 SNPs
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
Working space: 120 samples, 8723 SNPs
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
Working space: 120 samples, 8723 SNPs
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
Working space: 120 samples, 8723 SNPs
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
Working space: 120 samples, 8723 SNPs
Method: IBS
Output: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\tmp.gds
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
FUNCTION: snpgdsSNPList
FUNCTION: snpgdsSNPListClass
FUNCTION: snpgdsSNPListIntersect
FUNCTION: snpgdsSNPRateFreq
FUNCTION: snpgdsSampMissRate
FUNCTION: snpgdsSelectSNP
Excluding 365 SNPs on non-autosomes
Excluding 1,221 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.95)
FUNCTION: snpgdsSlidingWindow
Sliding Window Analysis:
Excluding 8 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 9,080 SNPs
using 1 (CPU) core
window size: 500000, shift: 100000 (basepair)
Chromosome Set: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23
Sat Apr 13 05:42:33 2019, Chromosome 1 (716 SNPs), 2448 windows
Sat Apr 13 05:42:33 2019, Chromosome 2 (742 SNPs), 2416 windows
Sat Apr 13 05:42:34 2019, Chromosome 3 (609 SNPs), 1985 windows
Sat Apr 13 05:42:34 2019, Chromosome 4 (562 SNPs), 1894 windows
Sat Apr 13 05:42:34 2019, Chromosome 5 (566 SNPs), 1797 windows
Sat Apr 13 05:42:34 2019, Chromosome 6 (565 SNPs), 1694 windows
Sat Apr 13 05:42:34 2019, Chromosome 7 (472 SNPs), 1573 windows
Sat Apr 13 05:42:34 2019, Chromosome 8 (488 SNPs), 1445 windows
Sat Apr 13 05:42:34 2019, Chromosome 9 (416 SNPs), 1393 windows
Sat Apr 13 05:42:34 2019, Chromosome 10 (483 SNPs), 1343 windows
Sat Apr 13 05:42:34 2019, Chromosome 11 (447 SNPs), 1338 windows
Sat Apr 13 05:42:34 2019, Chromosome 12 (427 SNPs), 1316 windows
Sat Apr 13 05:42:34 2019, Chromosome 13 (344 SNPs), 948 windows
Sat Apr 13 05:42:34 2019, Chromosome 14 (281 SNPs), 847 windows
Sat Apr 13 05:42:34 2019, Chromosome 15 (262 SNPs), 774 windows
Sat Apr 13 05:42:34 2019, Chromosome 16 (278 SNPs), 873 windows
Sat Apr 13 05:42:34 2019, Chromosome 17 (207 SNPs), 773 windows
Sat Apr 13 05:42:34 2019, Chromosome 18 (266 SNPs), 753 windows
Sat Apr 13 05:42:34 2019, Chromosome 19 (120 SNPs), 627 windows
Sat Apr 13 05:42:34 2019, Chromosome 20 (229 SNPs), 602 windows
Sat Apr 13 05:42:34 2019, Chromosome 21 (126 SNPs), 311 windows
Sat Apr 13 05:42:34 2019, Chromosome 22 (116 SNPs), 312 windows
Sat Apr 13 05:42:34 2019, Chromosome 23 (358 SNPs), 1507 windows
Sat Apr 13 05:42:34 2019 Done.
FUNCTION: snpgdsSummary
The file name: C:\Users\biocbuild\bbs-3.8-bioc\R\library\SNPRelate\extdata\hapmap_geno.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsTranspose
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
SNP genotypes: 279 samples, 9088 SNPs
Genotype matrix is being transposed ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 28
save to 'test.gds.tmp'
rename 'test.gds.tmp' (709.6K, reduced: 619.1K)
# of fragments: 26
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in individual-major mode (SNP X Sample).
FUNCTION: snpgdsVCF2GDS
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
VCF Format ==> SNP GDS Format
Method: exacting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test1.gds' (2.9K)
# of fragments: 46
save to 'test1.gds.tmp'
rename 'test1.gds.tmp' (2.6K, reduced: 312B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
VCF Format ==> SNP GDS Format
Method: exacting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
SNP genotypes: 3 samples, 2 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test2.gds' (3.0K)
# of fragments: 48
save to 'test2.gds.tmp'
rename 'test2.gds.tmp' (2.6K, reduced: 417B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in individual-major mode (SNP X Sample).
VCF Format ==> SNP GDS Format
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
SNP genotypes: 3 samples, 5 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test3.gds' (3.1K)
# of fragments: 48
save to 'test3.gds.tmp'
rename 'test3.gds.tmp' (2.7K, reduced: 419B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in individual-major mode (SNP X Sample).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
VCF Format ==> SNP GDS Format
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test4.gds' (3.0K)
# of fragments: 46
save to 'test4.gds.tmp'
rename 'test4.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
VCF Format ==> SNP GDS Format
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test5.gds' (3.0K)
# of fragments: 46
save to 'test5.gds.tmp'
rename 'test5.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., T/A,G).
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test5.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
FUNCTION: snpgdsVCF2GDS_R
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Apr 13 05:42:34 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Sat Apr 13 05:42:35 2019 Done.
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Apr 13 05:42:35 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Sat Apr 13 05:42:35 2019 Done.
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Apr 13 05:42:35 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
Sat Apr 13 05:42:35 2019 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Apr 13 05:42:35 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
Sat Apr 13 05:42:35 2019 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_i386\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
SNP Correlation:
Working space: 90 samples, 9088 SNPs
using 1 (CPU) core
using the top 2 eigenvectors
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Apr 13 05:42:37 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:37 2019 Done.
SNP Correlation:
Working space: 90 samples, 9088 SNPs
using 1 (CPU) core
using the top 2 eigenvectors
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Apr 13 05:42:37 2019
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:37 2019 Done.
SNP loading:
Working space: 90 samples, 8695 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Sat Apr 13 05:42:37 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:37 2019 Done.
Sample loading:
Working space: 100 samples, 8695 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Sat Apr 13 05:42:37 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:37 2019 Done.
SNP Correlation:
Working space: 90 samples, 9088 SNPs
using 2 (CPU) cores
using the top 2 eigenvectors
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Apr 13 05:42:37 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:37 2019 Done.
SNP Correlation:
Working space: 90 samples, 9088 SNPs
using 2 (CPU) cores
using the top 2 eigenvectors
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Apr 13 05:42:37 2019
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:37 2019 Done.
SNP loading:
Working space: 90 samples, 8695 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Sat Apr 13 05:42:37 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:37 2019 Done.
Sample loading:
Working space: 100 samples, 8695 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Sat Apr 13 05:42:37 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:37 2019 Done.
RUNIT TEST PROTOCOL -- Sat Apr 13 05:42:38 2019
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
SNPRelate RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
65.21 2.10 67.64
|
SNPRelate.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("SNPRelate")
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Genetic Relationship Matrix (GRM, GCTA):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 1,000 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:39 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:40 2019 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 2,000 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:40 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:41 2019 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 3,800 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:41 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:42 2019 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 6,800 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:42 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:43 2019 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 1,000 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:43 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:43 2019 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 2,000 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:43 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:44 2019 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 3,800 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:44 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:45 2019 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Writing ...
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 6,800 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:45 2019 (internal increment: 65536)
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Sat Apr 13 05:42:46 2019 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 279 samples, 1000 SNPs
using 1 (CPU) core.
method: covariance
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 279 samples, 1000 SNPs
using 1 (CPU) core.
method: correlation
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
FUNCTION: SNPGDSFileClass
FUNCTION: SNPRelate-package
Start snpgdsBED2GDS ...
BED file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz" in the SNP-major mode (Sample X SNP)
FAM file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz", DONE.
BIM file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz", DONE.
Sat Apr 13 05:42:50 2019 store sample id, snp id, position, and chromosome.
start writing: 60 samples, 5000 SNPs ...
Sat Apr 13 05:42:50 2019 0%
Sat Apr 13 05:42:50 2019 100%
Sat Apr 13 05:42:50 2019 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
Principal Component Analysis (PCA) on genotypes:
Excluding 203 SNPs on non-autosomes
Excluding 28 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 60 samples, 4,769 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 124273
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:50 2019 (internal increment: 53996)
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Sat Apr 13 05:42:50 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:42:50 2019 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
PLINK IBD: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:42:50 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:42:51 2019 Done.
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:42:51 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:51 2019 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 279 samples, 200 SNPs
using 1 (CPU) core.
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 55417
FUNCTION: hapmap_geno
FUNCTION: snpgdsAdmixPlot
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:52 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:52 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:42:53 2019 Done.
FUNCTION: snpgdsAdmixProp
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:53 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:53 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:42:53 2019 Done.
FUNCTION: snpgdsAlleleSwitch
Strand-switching at 50 SNP locus/loci.
Unable to determine switching at 10 SNP locus/loci.
FUNCTION: snpgdsApartSelection
Sat Apr 13 05:42:53 2019 Chromosome 1, # of SNPs: 365
Sat Apr 13 05:42:53 2019 Chromosome 2, # of SNPs: 370
Sat Apr 13 05:42:53 2019 Chromosome 3, # of SNPs: 314
Sat Apr 13 05:42:53 2019 Chromosome 4, # of SNPs: 294
Sat Apr 13 05:42:53 2019 Chromosome 5, # of SNPs: 291
Sat Apr 13 05:42:53 2019 Chromosome 6, # of SNPs: 280
Sat Apr 13 05:42:53 2019 Chromosome 7, # of SNPs: 245
Sat Apr 13 05:42:53 2019 Chromosome 8, # of SNPs: 232
Sat Apr 13 05:42:53 2019 Chromosome 9, # of SNPs: 203
Sat Apr 13 05:42:53 2019 Chromosome 10, # of SNPs: 224
Sat Apr 13 05:42:53 2019 Chromosome 11, # of SNPs: 227
Sat Apr 13 05:42:53 2019 Chromosome 12, # of SNPs: 215
Sat Apr 13 05:42:53 2019 Chromosome 13, # of SNPs: 175
Sat Apr 13 05:42:53 2019 Chromosome 14, # of SNPs: 147
Sat Apr 13 05:42:53 2019 Chromosome 15, # of SNPs: 127
Sat Apr 13 05:42:53 2019 Chromosome 16, # of SNPs: 128
Sat Apr 13 05:42:53 2019 Chromosome 17, # of SNPs: 112
Sat Apr 13 05:42:53 2019 Chromosome 18, # of SNPs: 127
Sat Apr 13 05:42:53 2019 Chromosome 19, # of SNPs: 76
Sat Apr 13 05:42:53 2019 Chromosome 20, # of SNPs: 107
Sat Apr 13 05:42:53 2019 Chromosome 21, # of SNPs: 63
Sat Apr 13 05:42:53 2019 Chromosome 22, # of SNPs: 54
Sat Apr 13 05:42:53 2019 Chromosome 23, # of SNPs: 215
Total # of SNPs selected:4591
FUNCTION: snpgdsBED2GDS
Start snpgdsBED2GDS ...
BED file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz" in the SNP-major mode (Sample X SNP)
FAM file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz", DONE.
BIM file: "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz", DONE.
Sat Apr 13 05:42:53 2019 store sample id, snp id, position, and chromosome.
start writing: 60 samples, 5000 SNPs ...
Sat Apr 13 05:42:53 2019 0%
Sat Apr 13 05:42:53 2019 100%
Sat Apr 13 05:42:53 2019 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
FUNCTION: snpgdsClose
FUNCTION: snpgdsCombineGeno
Create a GDS genotype file:
The new dataset consists of 10 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 20 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
10 samples, 3000 SNPs
open 't2.gds' ...
20 samples, 3000 SNPs
Concatenating samples (mapping to the first GDS file) ...
reference: 3000 SNPs (100.0%)
file 2: 0 allele flips, 0 ambiguous locus/loci
[no flip]: 3000
create 'test.gds': 30 samples, 3000 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (46.2K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (46.0K, reduced: 204B)
# of fragments: 15
Done.
Create a GDS genotype file:
The new dataset consists of 279 samples and 100 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 279 samples and 200 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
279 samples, 100 SNPs
open 't2.gds' ...
279 samples, 200 SNPs
Concatenating SNPs ...
create 'test.gds': 279 samples, 300 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (19.1K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (18.9K, reduced: 204B)
# of fragments: 15
Done.
FUNCTION: snpgdsCreateGeno
Principal Component Analysis (PCA) on genotypes:
Excluding 42 SNPs on non-autosomes
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 958 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 264760
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:42:54 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:42:54 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:42:54 2019 Done.
FUNCTION: snpgdsCreateGenoSet
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 75.42%, 540/716
Chromosome 2: 72.24%, 536/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.31%, 412/562
Chromosome 5: 77.03%, 436/566
Chromosome 6: 75.58%, 427/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.31%, 348/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.33%, 359/483
Chromosome 11: 77.40%, 346/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 75.58%, 260/344
Chromosome 14: 76.95%, 217/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 74.40%, 154/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,547 markers are selected in total.
Create a GDS genotype file:
The new dataset consists of 279 samples and 6547 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsCutTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Apr 13 05:42:55 2019 0%
Dissimilarity: Sat Apr 13 05:42:56 2019 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
Create 4 groups.
FUNCTION: snpgdsDiss
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Apr 13 05:42:57 2019 0%
Dissimilarity: Sat Apr 13 05:42:58 2019 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsDrawTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Apr 13 05:42:59 2019 0%
Dissimilarity: Sat Apr 13 05:43:00 2019 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsEIGMIX
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:01 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:01 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:43:01 2019 Done.
FUNCTION: snpgdsErrMsg
FUNCTION: snpgdsExampleFileName
FUNCTION: snpgdsFst
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
Method: Weir & Cockerham, 1984
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
Method: Weir & Hill, 2002
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
FUNCTION: snpgdsGDS2BED
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to PLINK binary PED:
Working space: 279 samples, 8722 SNPs
Output a BIM file.
Output a BED file ...
Sat Apr 13 05:43:02 2019 0%
Sat Apr 13 05:43:02 2019 100%
Done.
FUNCTION: snpgdsGDS2Eigen
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to EIGENSOFT:
save to *.snp: 8722 snps
save to *.ind: 279 samples
Output: Sat Apr 13 05:43:02 2019 0%
Output: Sat Apr 13 05:43:02 2019 100%
Done.
FUNCTION: snpgdsGDS2PED
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Sat Apr 13 05:43:02 2019 0%
Output: Sat Apr 13 05:43:02 2019 100%
FUNCTION: snpgdsGEN2GDS
running snpgdsGEN2GDS ...
FUNCTION: snpgdsGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:02 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:43:03 2019 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:03 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:04 2019 Done.
FUNCTION: snpgdsGetGeno
Genotype matrix: 1000 SNPs X 279 samples
Genotype matrix: 279 samples X 1000 SNPs
FUNCTION: snpgdsHCluster
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Apr 13 05:43:04 2019 0%
Dissimilarity: Sat Apr 13 05:43:05 2019 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsHWE
Keeping 716 SNPs according to chromosome 1
Excluding 160 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
FUNCTION: snpgdsIBDKING
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:06 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:06 2019 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:06 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:06 2019 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
# of families: 20, and within- and between-family relationship are estimated differently.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:07 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:07 2019 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Apr 13 05:43:07 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:07 2019 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Apr 13 05:43:07 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:43:08 2019 Done.
FUNCTION: snpgdsIBDMLE
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
Working space: 30 samples, 7,142 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.45%, 404/742
Chromosome 3: 55.67%, 339/609
Chromosome 4: 56.94%, 320/562
Chromosome 5: 56.71%, 321/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 55.72%, 263/472
Chromosome 8: 50.41%, 246/488
Chromosome 9: 54.33%, 226/416
Chromosome 10: 50.10%, 242/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 55.04%, 235/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 55.67%, 157/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 52.84%, 121/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 50.86%, 59/116
4,754 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 30 samples, 250 SNPs
using 1 (CPU) core
MLE IBD: the sum of all selected genotypes (0,1,2) = 7195
MLE IBD: Sat Apr 13 05:43:08 2019 0%
MLE IBD: Sat Apr 13 05:43:09 2019 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.480, sd: 0.281
MLE IBD: the sum of all selected genotypes (0,1,2) = 5991
MLE IBD: Sat Apr 13 05:43:09 2019 0%
MLE IBD: Sat Apr 13 05:43:09 2019 100%
FUNCTION: snpgdsIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
Working space: 30 samples, 7,142 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.45%, 404/742
Chromosome 3: 55.67%, 339/609
Chromosome 4: 56.94%, 320/562
Chromosome 5: 56.71%, 321/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 55.72%, 263/472
Chromosome 8: 50.41%, 246/488
Chromosome 9: 54.33%, 226/416
Chromosome 10: 50.10%, 242/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 55.04%, 235/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 55.67%, 157/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 52.84%, 121/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 50.86%, 59/116
4,754 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 30 samples, 250 SNPs
using 1 (CPU) core
MLE IBD: the sum of all selected genotypes (0,1,2) = 7195
MLE IBD: Sat Apr 13 05:43:09 2019 0%
MLE IBD: Sat Apr 13 05:43:10 2019 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.480, sd: 0.281
MLE IBD: the sum of all selected genotypes (0,1,2) = 5991
MLE IBD: Sat Apr 13 05:43:10 2019 0%
MLE IBD: Sat Apr 13 05:43:10 2019 100%
FUNCTION: snpgdsIBDMoM
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 92 samples, 7,506 SNPs
using 1 (CPU) core
PLINK IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Apr 13 05:43:11 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:11 2019 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 93 samples, 8,160 SNPs
using 1 (CPU) core
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Apr 13 05:43:11 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:11 2019 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 93 samples, 8,160 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Apr 13 05:43:11 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:11 2019 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 8,160 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 203285
Sat Apr 13 05:43:11 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:11 2019 Done.
FUNCTION: snpgdsIBDSelection
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 93 samples, 8,160 SNPs
using 1 (CPU) core
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Apr 13 05:43:11 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:11 2019 Done.
FUNCTION: snpgdsIBS
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:43:11 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:11 2019 Done.
FUNCTION: snpgdsIBSNum
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:43:11 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:43:12 2019 Done.
FUNCTION: snpgdsIndInb
Estimating individual inbreeding coefficients:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
FUNCTION: snpgdsIndInbCoef
FUNCTION: snpgdsIndivBeta
Individual Inbreeding and Relatedness (beta estimator):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
Individual Beta: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:12 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:12 2019 Done.
FUNCTION: snpgdsLDMat
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 279 samples, 203 SNPs
using 1 (CPU) core.
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
Linkage Disequilibrium (LD) estimation on genotypes:
Working space: 279 samples, 203 SNPs
using 1 (CPU) core.
sliding window size: 203
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
FUNCTION: snpgdsLDpair
FUNCTION: snpgdsLDpruning
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 75.42%, 540/716
Chromosome 2: 72.24%, 536/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.31%, 412/562
Chromosome 5: 77.03%, 436/566
Chromosome 6: 75.58%, 427/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.31%, 348/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.33%, 359/483
Chromosome 11: 77.40%, 346/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 75.58%, 260/344
Chromosome 14: 76.95%, 217/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 74.40%, 154/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,547 markers are selected in total.
FUNCTION: snpgdsMergeGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 6,800 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:13 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:13 2019 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 3,400 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 951558
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:13 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:43:14 2019 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 3,400 SNPs
using 1 (CPU) core
GRM Calculation: the sum of all selected genotypes (0,1,2) = 957408
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:14 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:14 2019 Done.
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
FUNCTION: snpgdsOpen
FUNCTION: snpgdsOption
FUNCTION: snpgdsPCA
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:15 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:15 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:43:15 2019 Done.
FUNCTION: snpgdsPCACorr
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:15 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:43:16 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:43:16 2019 Done.
SNP Correlation:
Working space: 279 samples, 9088 SNPs
using 1 (CPU) core
using the top 4 eigenvectors
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Sat Apr 13 05:43:16 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:16 2019 Done.
SNP Correlation:
Working space: 279 samples, 9088 SNPs
using 1 (CPU) core
using the top 4 eigenvectors
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Sat Apr 13 05:43:16 2019
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:16 2019 Done.
FUNCTION: snpgdsPCASNPLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:16 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:16 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:43:16 2019 Done.
SNP loading:
Working space: 279 samples, 8722 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:43:16 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 1s
Sat Apr 13 05:43:17 2019 Done.
FUNCTION: snpgdsPCASampLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 8,722 SNPs
using 1 (CPU) core
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Apr 13 05:43:17 2019 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:17 2019 Begin (eigenvalues and eigenvectors)
Sat Apr 13 05:43:17 2019 Done.
SNP loading:
Working space: 279 samples, 8722 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Sat Apr 13 05:43:17 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:17 2019 Done.
Sample loading:
Working space: 100 samples, 8722 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 878146
Sat Apr 13 05:43:17 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:17 2019 Done.
FUNCTION: snpgdsPED2GDS
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Sat Apr 13 05:43:17 2019 0%
Output: Sat Apr 13 05:43:17 2019 100%
PLINK PED/MAP to GDS Format:
Import 9088 variants from 'tmp.map'
Chromosome:
1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7
716 483 447 427 344 282 262 278 207 266 120 742 229 126 116 609 562 566 565 472
8 9 X
488 416 365
Reading 'tmp.ped'
Output: 'test.gds'
Import 279 samples
Transpose the genotypic matrix ...
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 50
save to 'test.gds.tmp'
rename 'test.gds.tmp' (711.4K, reduced: 618.7K)
# of fragments: 26
FUNCTION: snpgdsPairIBD
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
Working space: 93 samples, 7,077 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.40%, 463/742
Chromosome 3: 60.76%, 370/609
Chromosome 4: 64.59%, 363/562
Chromosome 5: 62.54%, 354/566
Chromosome 6: 60.00%, 339/565
Chromosome 7: 62.71%, 296/472
Chromosome 8: 58.61%, 286/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.66%, 293/483
Chromosome 11: 62.86%, 281/447
Chromosome 12: 63.00%, 269/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.48%, 179/282
Chromosome 15: 63.36%, 166/262
Chromosome 16: 61.87%, 172/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.02%, 157/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 67.25%, 154/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,429 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.506, sd: 0.300
MLE IBD: the sum of all selected genotypes (0,1,2) = 6339
MLE IBD: Sat Apr 13 05:43:18 2019 0%
MLE IBD: Sat Apr 13 05:43:19 2019 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.506, sd: 0.300
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6339
Sat Apr 13 05:43:19 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:19 2019 Done.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.506, sd: 0.300
MLE IBD: the sum of all selected genotypes (0,1,2) = 6339
MLE IBD: Sat Apr 13 05:43:19 2019 0%
MLE IBD: Sat Apr 13 05:43:20 2019 100%
Genotype matrix: 250 SNPs X 25 samples
[1] -364.4667
[1] -377.9771
[1] -390.3299
[1] -380.5342
[1] -378.2092
[1] -383.641
[1] -364.5406
[1] -375.196
[1] -383.5752
[1] -385.7771
[1] -368.6237
[1] -390.7766
[1] -367.5082
[1] -383.595
[1] -385.7602
[1] -378.5134
[1] -388.3292
[1] -376.4419
[1] -378.3509
[1] -386.8318
[1] -385.3803
[1] -382.988
[1] -369.9328
[1] -383.3912
FUNCTION: snpgdsPairIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
Working space: 93 samples, 7,077 SNPs
using 1 (CPU) core
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.40%, 463/742
Chromosome 3: 60.76%, 370/609
Chromosome 4: 64.59%, 363/562
Chromosome 5: 62.54%, 354/566
Chromosome 6: 60.00%, 339/565
Chromosome 7: 62.71%, 296/472
Chromosome 8: 58.61%, 286/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.66%, 293/483
Chromosome 11: 62.86%, 281/447
Chromosome 12: 63.00%, 269/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.48%, 179/282
Chromosome 15: 63.36%, 166/262
Chromosome 16: 61.87%, 172/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.02%, 157/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 67.25%, 154/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,429 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.506, sd: 0.300
MLE IBD: the sum of all selected genotypes (0,1,2) = 6339
MLE IBD: Sat Apr 13 05:43:20 2019 0%
MLE IBD: Sat Apr 13 05:43:21 2019 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 25 samples, 250 SNPs
using 1 (CPU) core
Specifying allele frequencies, mean: 0.506, sd: 0.300
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6339
Sat Apr 13 05:43:21 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:21 2019 Done.
Genotype matrix: 250 SNPs X 25 samples
[1] -364.4667
[1] -377.9771
[1] -390.3299
[1] -380.5342
[1] -378.2092
[1] -383.641
[1] -364.5406
[1] -375.196
[1] -383.5752
[1] -385.7771
[1] -368.6237
[1] -390.7766
[1] -367.5082
[1] -383.595
[1] -385.7602
[1] -378.5134
[1] -388.3292
[1] -376.4419
[1] -378.3509
[1] -386.8318
[1] -385.3803
[1] -382.988
[1] -369.9328
[1] -383.3912
FUNCTION: snpgdsPairScore
Excluding 365 SNPs on non-autosomes
Working space: 120 samples, 8723 SNPs
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
Working space: 120 samples, 8723 SNPs
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
Working space: 120 samples, 8723 SNPs
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
Working space: 120 samples, 8723 SNPs
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
Working space: 120 samples, 8723 SNPs
Method: IBS
Output: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\tmp.gds
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
FUNCTION: snpgdsSNPList
FUNCTION: snpgdsSNPListClass
FUNCTION: snpgdsSNPListIntersect
FUNCTION: snpgdsSNPRateFreq
FUNCTION: snpgdsSampMissRate
FUNCTION: snpgdsSelectSNP
Excluding 365 SNPs on non-autosomes
Excluding 1,221 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.95)
FUNCTION: snpgdsSlidingWindow
Sliding Window Analysis:
Excluding 8 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
Working space: 279 samples, 9,080 SNPs
using 1 (CPU) core
window size: 500000, shift: 100000 (basepair)
Chromosome Set: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23
Sat Apr 13 05:43:22 2019, Chromosome 1 (716 SNPs), 2448 windows
Sat Apr 13 05:43:22 2019, Chromosome 2 (742 SNPs), 2416 windows
Sat Apr 13 05:43:22 2019, Chromosome 3 (609 SNPs), 1985 windows
Sat Apr 13 05:43:22 2019, Chromosome 4 (562 SNPs), 1894 windows
Sat Apr 13 05:43:22 2019, Chromosome 5 (566 SNPs), 1797 windows
Sat Apr 13 05:43:22 2019, Chromosome 6 (565 SNPs), 1694 windows
Sat Apr 13 05:43:22 2019, Chromosome 7 (472 SNPs), 1573 windows
Sat Apr 13 05:43:22 2019, Chromosome 8 (488 SNPs), 1445 windows
Sat Apr 13 05:43:22 2019, Chromosome 9 (416 SNPs), 1393 windows
Sat Apr 13 05:43:22 2019, Chromosome 10 (483 SNPs), 1343 windows
Sat Apr 13 05:43:22 2019, Chromosome 11 (447 SNPs), 1338 windows
Sat Apr 13 05:43:22 2019, Chromosome 12 (427 SNPs), 1316 windows
Sat Apr 13 05:43:22 2019, Chromosome 13 (344 SNPs), 948 windows
Sat Apr 13 05:43:22 2019, Chromosome 14 (281 SNPs), 847 windows
Sat Apr 13 05:43:22 2019, Chromosome 15 (262 SNPs), 774 windows
Sat Apr 13 05:43:22 2019, Chromosome 16 (278 SNPs), 873 windows
Sat Apr 13 05:43:22 2019, Chromosome 17 (207 SNPs), 773 windows
Sat Apr 13 05:43:22 2019, Chromosome 18 (266 SNPs), 753 windows
Sat Apr 13 05:43:22 2019, Chromosome 19 (120 SNPs), 627 windows
Sat Apr 13 05:43:22 2019, Chromosome 20 (229 SNPs), 602 windows
Sat Apr 13 05:43:22 2019, Chromosome 21 (126 SNPs), 311 windows
Sat Apr 13 05:43:22 2019, Chromosome 22 (116 SNPs), 312 windows
Sat Apr 13 05:43:22 2019, Chromosome 23 (358 SNPs), 1507 windows
Sat Apr 13 05:43:22 2019 Done.
FUNCTION: snpgdsSummary
The file name: C:\Users\biocbuild\bbs-3.8-bioc\R\library\SNPRelate\extdata\hapmap_geno.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsTranspose
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
SNP genotypes: 279 samples, 9088 SNPs
Genotype matrix is being transposed ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 28
save to 'test.gds.tmp'
rename 'test.gds.tmp' (709.6K, reduced: 619.1K)
# of fragments: 26
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in individual-major mode (SNP X Sample).
FUNCTION: snpgdsVCF2GDS
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
VCF Format ==> SNP GDS Format
Method: exacting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test1.gds' (2.9K)
# of fragments: 46
save to 'test1.gds.tmp'
rename 'test1.gds.tmp' (2.6K, reduced: 312B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
VCF Format ==> SNP GDS Format
Method: exacting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
SNP genotypes: 3 samples, 2 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test2.gds' (3.0K)
# of fragments: 48
save to 'test2.gds.tmp'
rename 'test2.gds.tmp' (2.6K, reduced: 417B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in individual-major mode (SNP X Sample).
VCF Format ==> SNP GDS Format
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
SNP genotypes: 3 samples, 5 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test3.gds' (3.1K)
# of fragments: 48
save to 'test3.gds.tmp'
rename 'test3.gds.tmp' (2.7K, reduced: 419B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in individual-major mode (SNP X Sample).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
VCF Format ==> SNP GDS Format
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test4.gds' (3.0K)
# of fragments: 46
save to 'test4.gds.tmp'
rename 'test4.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
VCF Format ==> SNP GDS Format
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test5.gds' (3.0K)
# of fragments: 46
save to 'test5.gds.tmp'
rename 'test5.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., T/A,G).
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test5.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
FUNCTION: snpgdsVCF2GDS_R
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Apr 13 05:43:23 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Sat Apr 13 05:43:23 2019 Done.
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Apr 13 05:43:23 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Sat Apr 13 05:43:23 2019 Done.
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Apr 13 05:43:23 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
Sat Apr 13 05:43:23 2019 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Apr 13 05:43:23 2019 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPRelate/extdata/sequence.vcf
Sat Apr 13 05:43:23 2019 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.8-bioc\meat\SNPRelate.Rcheck\tests_x64\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
SNP Correlation:
Working space: 90 samples, 9088 SNPs
using 1 (CPU) core
using the top 2 eigenvectors
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Apr 13 05:43:24 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:24 2019 Done.
SNP Correlation:
Working space: 90 samples, 9088 SNPs
using 1 (CPU) core
using the top 2 eigenvectors
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Apr 13 05:43:24 2019
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:24 2019 Done.
SNP loading:
Working space: 90 samples, 8695 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Sat Apr 13 05:43:24 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:24 2019 Done.
Sample loading:
Working space: 100 samples, 8695 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Sat Apr 13 05:43:24 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:24 2019 Done.
SNP Correlation:
Working space: 90 samples, 9088 SNPs
using 2 (CPU) cores
using the top 2 eigenvectors
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Apr 13 05:43:24 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:24 2019 Done.
SNP Correlation:
Working space: 90 samples, 9088 SNPs
using 2 (CPU) cores
using the top 2 eigenvectors
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Apr 13 05:43:24 2019
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:24 2019 Done.
SNP loading:
Working space: 90 samples, 8695 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Sat Apr 13 05:43:24 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:24 2019 Done.
Sample loading:
Working space: 100 samples, 8695 SNPs
using 1 (CPU) core
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Sat Apr 13 05:43:24 2019 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Sat Apr 13 05:43:24 2019 Done.
RUNIT TEST PROTOCOL -- Sat Apr 13 05:43:24 2019
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
SNPRelate RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
44.21 2.17 46.17
|
