Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GWASTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GWASTools_1.56.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GWASTools.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-apple-darwin20* R was compiled by    Apple clang version 14.0.0 (clang-1400.0.29.202)    GNU Fortran (GCC) 14.2.0* running under: macOS Monterey 12.7.6* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘GWASTools/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘GWASTools’ version ‘1.56.0’* checking package namespace information ... OK* checking package dependencies ... OK* checking if this is a source package ... OK* checking if there is a namespace ... OK* checking for hidden files and directories ... OK* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package ‘GWASTools’ can be installed ... OK* checking installed package size ... OK* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... OK* checking top-level files ... OK* checking for left-over files ... OK* checking index information ... OK* checking package subdirectories ... OK* checking code files for non-ASCII characters ... OK* checking R files for syntax errors ... OK* checking whether the package can be loaded ... OK* checking whether the package can be loaded with stated dependencies ... OK* checking whether the package can be unloaded cleanly ... OK* checking whether the namespace can be loaded with stated dependencies ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking dependencies in R code ... NOTEUnexported object imported by a ':::' call: ‘S4Vectors:::make_zero_col_DataFrame’  See the note in ?`:::` about the use of this operator.* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... OK* checking Rd files ... NOTEcheckRd: (-1) imputedDosageFile.Rd:95: Lost braces in \itemize; meant \describe ?checkRd: (-1) imputedDosageFile.Rd:96: Lost braces in \itemize; meant \describe ?checkRd: (-1) imputedDosageFile.Rd:97: Lost braces in \itemize; meant \describe ?* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  BAFfromClusterMeans.Rd: add.gdsn  BAFfromGenotypes.Rd: add.gdsn  GWASTools-package.Rd: AnnotatedDataFrame  GdsReader-class.Rd: put.attr.gdsn, gdsfmt  ScanAnnotationDataFrame-class.Rd: AnnotatedDataFrame  SnpAnnotationDataFrame-class.Rd: AnnotatedDataFrame  anomDetectBAF.Rd: smooth.CNA, DNAcopy, segment  anomDetectLOH.Rd: smooth.CNA, DNAcopy, segment  anomIdentifyLowQuality.Rd: DNAcopy  assocCoxPH.Rd: Surv, coxph, survival  assocRegression.Rd: logistf, vcovHC, lrtest  convertNcdfGds.Rd: add.gdsn, gdsfmt  createDataFile.Rd: add.gdsn, gdsfmt  exactHWE.Rd: HWExact, GWASExactHW  gdsSubset.Rd: add.gdsn, gdsfmt  imputedDosageFile.Rd: add.gdsn  setMissingGenotypes.Rd: add.gdsnPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... OK* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking contents of ‘data’ directory ... OK* checking data for non-ASCII characters ... OK* checking LazyData ... OK* checking data for ASCII and uncompressed saves ... OK* checking sizes of PDF files under ‘inst/doc’ ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                         user system elapsedvcfWrite               24.132  1.096  25.974simulateGenotypeMatrix  0.979  0.187   9.543* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘test.R’ OK* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking running R code from vignettes ... SKIPPED* checking re-building of vignette outputs ... SKIPPED* checking PDF version of manual ... OK* DONEStatus: 3 NOTEsSee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/GWASTools.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GWASTools###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’* installing *source* package ‘GWASTools’ ...** this is package ‘GWASTools’ version ‘1.56.0’** using staged installation** R** data*** moving datasets to lazyload DB** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (GWASTools)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-apple-darwin20R 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.> library(GWASdata)Loading required package: GWASToolsLoading required package: BiobaseLoading required package: BiocGenericsLoading required package: genericsAttaching package: 'generics'The following objects are masked from 'package:base':    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,    setequal, unionAttaching package: 'BiocGenerics'The following objects are masked from 'package:stats':    IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,    as.data.frame, basename, cbind, colnames, dirname, do.call,    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,    unsplit, which.max, which.minWelcome to Bioconductor    Vignettes contain introductory material; view with    'browseVignettes()'. To cite Bioconductor, see    'citation("Biobase")', and for packages 'citation("pkgname")'.> library(ncdf4)> library(gdsfmt)> BiocGenerics:::testPackage("GWASTools", pattern=".*_test\\.R$")block 1 of 1adding variables: quality, X, YClean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401b72b846' (67.1K)    # of fragments: 35    save to '/private/tmp/RtmperfYBE/file17a401b72b846.tmp'    rename '/private/tmp/RtmperfYBE/file17a401b72b846.tmp' (66.9K, reduced: 216B)    # of fragments: 17adding variables: quality, X, YClean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4042df9d5e' (67.1K)    # of fragments: 35    save to '/private/tmp/RtmperfYBE/file17a4042df9d5e.tmp'    rename '/private/tmp/RtmperfYBE/file17a4042df9d5e.tmp' (66.9K, reduced: 216B)    # of fragments: 17Analyzing: X280 Analyzing: X281 Analyzing: X280 Analyzing: X281 Analyzing: X280 Analyzing: X281 Fri Dec 12 05:41:17 2025 Chromosome 1Fri Dec 12 05:41:17 2025 Chromosome 2Fri Dec 12 05:41:17 2025 Chromosome 3Fri Dec 12 05:41:17 2025 Chromosome 4Fri Dec 12 05:41:17 2025 Chromosome 5Fri Dec 12 05:41:17 2025 Chromosome 6Fri Dec 12 05:41:17 2025 Chromosome 7Fri Dec 12 05:41:17 2025 Chromosome 8Fri Dec 12 05:41:17 2025 Chromosome 9Fri Dec 12 05:41:17 2025 Chromosome 10Fri Dec 12 05:41:17 2025 Chromosome 11Fri Dec 12 05:41:17 2025 Chromosome 12Fri Dec 12 05:41:17 2025 Chromosome 13Fri Dec 12 05:41:17 2025 Chromosome 14Fri Dec 12 05:41:17 2025 Chromosome 15Fri Dec 12 05:41:17 2025 Chromosome 16Fri Dec 12 05:41:17 2025 Chromosome 17Fri Dec 12 05:41:17 2025 Chromosome 18Fri Dec 12 05:41:17 2025 Chromosome 19Fri Dec 12 05:41:17 2025 Chromosome 20Fri Dec 12 05:41:17 2025 Chromosome 21Fri Dec 12 05:41:17 2025 Chromosome 22Fri Dec 12 05:41:17 2025 Chromosome 23Fri Dec 12 05:41:17 2025 Chromosome 24Fri Dec 12 05:41:17 2025 Chromosome 25Fri Dec 12 05:41:17 2025 Chromosome 26Fri Dec 12 05:41:17 2025 Total # of SNPs selected: 7Fri Dec 12 05:41:17 2025 Chromosome 1Fri Dec 12 05:41:17 2025 Chromosome 2Fri Dec 12 05:41:17 2025 Chromosome 3Fri Dec 12 05:41:17 2025 Chromosome 4Fri Dec 12 05:41:17 2025 Chromosome 5Fri Dec 12 05:41:17 2025 Chromosome 6Fri Dec 12 05:41:17 2025 Chromosome 7Fri Dec 12 05:41:17 2025 Chromosome 8Fri Dec 12 05:41:17 2025 Chromosome 9Fri Dec 12 05:41:17 2025 Chromosome 10Fri Dec 12 05:41:17 2025 Chromosome 11Fri Dec 12 05:41:17 2025 Chromosome 12Fri Dec 12 05:41:17 2025 Chromosome 13Fri Dec 12 05:41:17 2025 Chromosome 14Fri Dec 12 05:41:17 2025 Chromosome 15Fri Dec 12 05:41:17 2025 Chromosome 16Fri Dec 12 05:41:17 2025 Chromosome 17Fri Dec 12 05:41:17 2025 Chromosome 18Fri Dec 12 05:41:17 2025 Chromosome 19Fri Dec 12 05:41:17 2025 Chromosome 20Fri Dec 12 05:41:17 2025 Chromosome 21Fri Dec 12 05:41:17 2025 Chromosome 22Fri Dec 12 05:41:17 2025 Chromosome 23Fri Dec 12 05:41:17 2025 Chromosome 24Fri Dec 12 05:41:17 2025 Chromosome 25Fri Dec 12 05:41:17 2025 Chromosome 26Fri Dec 12 05:41:17 2025 Total # of SNPs selected: 9Loading required package: VariantAnnotationLoading required package: MatrixGenericsLoading required package: matrixStatsAttaching package: 'matrixStats'The following objects are masked from 'package:Biobase':    anyMissing, rowMediansAttaching package: 'MatrixGenerics'The following objects are masked from 'package:matrixStats':    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,    colWeightedMeans, colWeightedMedians, colWeightedSds,    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,    rowWeightedSds, rowWeightedVarsThe following object is masked from 'package:Biobase':    rowMediansLoading required package: SeqinfoLoading required package: GenomicRangesLoading required package: stats4Loading required package: S4VectorsAttaching package: 'S4Vectors'The following object is masked from 'package:utils':    findMatchesThe following objects are masked from 'package:base':    I, expand.grid, unnameLoading required package: IRangesLoading required package: SummarizedExperimentLoading required package: RsamtoolsLoading required package: BiostringsLoading required package: XVectorAttaching package: 'Biostrings'The following object is masked from 'package:base':    strsplitAttaching package: 'VariantAnnotation'The following object is masked from 'package:base':    tabulateLoading required package: SNPRelateSNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)Reading in Phenotype and Covariate Data...Running analysis with 40 SamplesBeginning Calculations...Block 1 of 1 Completed - 1.127 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...[1] "hi"   LR.Stat    LR.pval 8.55400428 0.03584773 [1] "hi"  LR.Stat   LR.pval 1.6733633 0.6428719 [1] "hi"    LR.Stat     LR.pval 11.30391026  0.01019107 [1] "hi"  LR.Stat   LR.pval 3.5479450 0.3145968 [1] "hi"   LR.Stat    LR.pval 8.85703394 0.03125334 [1] "hi"  LR.Stat   LR.pval 4.5360542 0.2090968 [1] "hi"  LR.Stat   LR.pval 5.2442899 0.1547585 [1] "hi"  LR.Stat   LR.pval 2.6576472 0.4474727 [1] "hi"    LR.Stat     LR.pval 15.67110354  0.00132434 [1] "hi"  LR.Stat   LR.pval 1.7737546 0.6206628 [1] "hi"  LR.Stat   LR.pval 2.7135101 0.4379363 [1] "hi"  LR.Stat   LR.pval 2.4907942 0.4769571 [1] "hi"    LR.Stat     LR.pval 10.06391337  0.01803059 [1] "hi" LR.Stat  LR.pval 4.834600 0.184317 [1] "hi"   LR.Stat    LR.pval 6.85119755 0.07679492 [1] "hi"     LR.Stat      LR.pval 12.410321031  0.006101951 [1] "hi"  LR.Stat   LR.pval 5.9806637 0.1125548 [1] "hi"  LR.Stat   LR.pval 4.5674714 0.2063504 [1] "hi"    LR.Stat     LR.pval 10.29919824  0.01618679 [1] "hi"     LR.Stat      LR.pval 12.161441314  0.006850104 [1] "hi"   LR.Stat    LR.pval 8.85117856 0.03133641 [1] "hi"  LR.Stat   LR.pval 4.6736748 0.1973122 Block 1 of 1 Completed - 3.537 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...[1] "hi"     LR.Stat      LR.pval 1.567110e+01 7.536688e-05 [1] "hi"  LR.Stat   LR.pval 1.6624991 0.1972662 [1] "hi"   LR.Stat    LR.pval 8.38393977 0.00378551 Block 1 of 1 Completed - 3.387 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...Block 1 of 1 Completed - 1.363 secsReading in Phenotype and Covariate Data...Running analysis with 500 SamplesBeginning Calculations...Block 1 of 1 Completed - 1.491 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...Block 1 of 1 Completed - 1.495 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.5222 secsReading in Phenotype and Covariate Data...Running analysis with 23 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.3385 secsReading in Phenotype and Covariate Data...Running analysis with 23 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.3352 secsReading in Phenotype and Covariate Data...Reading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.3454 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...Block 1 of 4 Completed - 0.1224 secsBlock 2 of 4 Completed - 0.129 secsBlock 3 of 4 Completed - 0.1559 secsBlock 4 of 4 Completed - 0.004061 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.4742 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.4741 secsReading in Phenotype and Covariate Data...Running analysis with 40 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.9324 secsReading in Phenotype and Covariate Data...Running analysis with 40 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.4879 secsReading in Phenotype and Covariate Data...Running analysis with 40 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.6851 secsLoading required package: zooAttaching package: 'zoo'The following objects are masked from 'package:Rsamtools':    index, index<-The following objects are masked from 'package:base':    as.Date, as.Date.numericAttaching package: 'sandwich'The following object is masked from 'package:generics':    estfunReading in Phenotype and Covariate Data...Running analysis with 40 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.8256 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.325 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.1618 secsReading in Phenotype and Covariate Data...Running analysis with 50 SamplesBeginning Calculations...Block 1 of 1 Completed - 0.1646 secsFri Dec 12 05:42:06 2025Load genotype dataset ...Fri Dec 12 05:42:06 20251/2batch1Fri Dec 12 05:42:06 2025Load genotype dataset ...Fri Dec 12 05:42:06 20251/4batch1Fri Dec 12 05:42:06 20252/4batch2Fri Dec 12 05:42:06 20253/4batch3Fri Dec 12 05:42:06 20254/4batch4Fri Dec 12 05:42:07 2025Load genotype dataset ...Fri Dec 12 05:42:07 20251/4batch1Fri Dec 12 05:42:07 20252/4batch2Fri Dec 12 05:42:07 20253/4batch3Fri Dec 12 05:42:07 20254/4batch4Fri Dec 12 05:42:07 2025Load genotype dataset ...Fri Dec 12 05:42:07 20251/4batch1Fri Dec 12 05:42:07 20252/4batch2Fri Dec 12 05:42:07 20253/4batch3Fri Dec 12 05:42:07 20254/4batch4Fri Dec 12 05:42:07 2025Load genotype dataset ...Fri Dec 12 05:42:07 20251/4batch1Fri Dec 12 05:42:07 20252/4batch2Fri Dec 12 05:42:07 20253/4batch3Fri Dec 12 05:42:07 20254/4batch4Fri Dec 12 05:42:07 2025Load genotype dataset ...Fri Dec 12 05:42:07 20251/4batch1Fri Dec 12 05:42:07 20252/4batch2Fri Dec 12 05:42:07 20253/4batch3Fri Dec 12 05:42:07 20254/4batch4Fri Dec 12 05:42:08 2025Load genotype dataset ...Fri Dec 12 05:42:08 20251/4batch1Fri Dec 12 05:42:08 20252/4batch2Fri Dec 12 05:42:08 20253/4batch3Fri Dec 12 05:42:08 20254/4batch4Fri Dec 12 05:42:08 2025Load genotype dataset ...Fri Dec 12 05:42:08 20251/4batch1Fri Dec 12 05:42:08 20252/4batch2Fri Dec 12 05:42:08 20253/4batch3Fri Dec 12 05:42:08 20254/4batch4Fri Dec 12 05:42:08 2025Load genotype dataset ...Fri Dec 12 05:42:08 20251/4batch1Fri Dec 12 05:42:08 20252/4batch2Fri Dec 12 05:42:08 20253/4batch3Fri Dec 12 05:42:08 20254/4batch4Fri Dec 12 05:42:08 2025Load genotype dataset ...Fri Dec 12 05:42:09 20251/2batch1Fri Dec 12 05:42:10 2025Load genotype dataset ...Fri Dec 12 05:42:10 20251/4batch1Fri Dec 12 05:42:10 20252/4batch2Fri Dec 12 05:42:11 20253/4batch3Fri Dec 12 05:42:11 20254/4batch4Fri Dec 12 05:42:11 2025Load genotype dataset ...Fri Dec 12 05:42:12 20251/2batch1Fri Dec 12 05:42:12 2025Load genotype dataset ...Fri Dec 12 05:42:12 20251/2batch1Fri Dec 12 05:42:12 2025Load genotype dataset ...Fri Dec 12 05:42:12 20251/2batch1Fri Dec 12 05:42:12 2025Load genotype dataset ...Fri Dec 12 05:42:13 20251/2batch1Fri Dec 12 05:42:13 2025Load genotype dataset ...Fri Dec 12 05:42:13 20251/2batch1Fri Dec 12 05:42:13 2025Load genotype dataset ...Fri Dec 12 05:42:13 20251/2batch1Fri Dec 12 05:42:13 2025Load genotype dataset ...Fri Dec 12 05:42:13 20251/2batch1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 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of 100Block 43 of 100Block 44 of 100Block 45 of 100Block 46 of 100Block 47 of 100Block 48 of 100Block 49 of 100Block 50 of 100Block 51 of 100Block 52 of 100Block 53 of 100Block 54 of 100Block 55 of 100Block 56 of 100Block 57 of 100Block 58 of 100Block 59 of 100Block 60 of 100Block 61 of 100Block 62 of 100Block 63 of 100Block 64 of 100Block 65 of 100Block 66 of 100Block 67 of 100Block 68 of 100Block 69 of 100Block 70 of 100Block 71 of 100Block 72 of 100Block 73 of 100Block 74 of 100Block 75 of 100Block 76 of 100Block 77 of 100Block 78 of 100Block 79 of 100Block 80 of 100Block 81 of 100Block 82 of 100Block 83 of 100Block 84 of 100Block 85 of 100Block 86 of 100Block 87 of 100Block 88 of 100Block 89 of 100Block 90 of 100Block 91 of 100Block 92 of 100Block 93 of 100Block 94 of 100Block 95 of 100Block 96 of 100Block 97 of 100Block 98 of 100Block 99 of 100Block 100 of 100Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 100Block 2 of 100Block 3 of 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100Block 71 of 100Block 72 of 100Block 73 of 100Block 74 of 100Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 100Block 2 of 100Block 3 of 100Block 4 of 100Block 5 of 100Block 6 of 100Block 7 of 100Block 8 of 100Block 9 of 100Block 10 of 100Block 11 of 100Block 12 of 100Block 13 of 100Block 14 of 100Block 15 of 100Block 16 of 100Block 17 of 100Block 18 of 100Block 19 of 100Block 20 of 100Block 21 of 100Block 22 of 100Block 23 of 100Block 24 of 100Block 25 of 100Block 26 of 100Block 27 of 100Block 28 of 100Block 29 of 100Block 30 of 100Block 31 of 100Block 32 of 100Block 33 of 100Block 34 of 100Block 35 of 100Block 36 of 100Block 37 of 100Block 38 of 100Block 39 of 100Block 40 of 100Block 41 of 100Block 42 of 100Block 43 of 100Block 44 of 100Block 45 of 100Block 46 of 100Block 47 of 100Block 48 of 100Block 49 of 100Block 50 of 100Block 51 of 100Block 52 of 100Block 53 of 100Block 54 of 100Block 55 of 100Block 56 of 100Block 57 of 100Block 58 of 100Block 59 of 100Block 60 of 100Block 61 of 100Block 62 of 100Block 63 of 100Block 64 of 100Block 65 of 100Block 66 of 100Block 67 of 100Block 68 of 100Block 69 of 100Block 70 of 100Block 71 of 100Block 72 of 100Block 73 of 100Block 74 of 100Block 75 of 100Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 100Block 2 of 100Block 3 of 100Block 4 of 100Block 5 of 100Block 6 of 100Block 7 of 100Block 8 of 100Block 9 of 100Block 10 of 100Block 11 of 100Block 12 of 100Block 13 of 100Block 14 of 100Block 15 of 100Block 16 of 100Block 17 of 100Block 18 of 100Block 19 of 100Block 20 of 100Block 21 of 100Block 22 of 100Block 23 of 100Block 24 of 100Block 25 of 100Block 26 of 100Block 27 of 100Block 28 of 100Block 29 of 100Block 30 of 100Block 31 of 100Block 32 of 100Block 33 of 100Block 34 of 100Block 35 of 100Block 36 of 100Block 37 of 100Block 38 of 100Block 39 of 100Block 40 of 100Block 41 of 100Block 42 of 100Block 43 of 100Block 44 of 100Block 45 of 100Block 46 of 100Block 47 of 100Block 48 of 100Block 49 of 100Block 50 of 100Block 51 of 100Block 52 of 100Block 53 of 100Block 54 of 100Block 55 of 100Block 56 of 100Block 57 of 100Block 58 of 100Block 59 of 100Block 60 of 100Block 61 of 100Block 62 of 100Block 63 of 100Block 64 of 100Block 65 of 100Block 66 of 100Block 67 of 100Block 68 of 100Block 69 of 100Block 70 of 100Block 71 of 100Block 72 of 100Block 73 of 100Block 74 of 100Block 75 of 100Block 76 of 100Block 77 of 100Block 78 of 100Block 79 of 100Block 80 of 100Block 81 of 100Block 82 of 100Block 83 of 100Block 84 of 100Block 85 of 100Block 86 of 100Block 87 of 100Block 88 of 100Block 89 of 100Block 90 of 100Block 91 of 100Block 92 of 100Block 93 of 100Block 94 of 100Block 95 of 100Block 96 of 100Block 97 of 100Block 98 of 100Block 99 of 100Block 100 of 100Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 100Block 2 of 100Block 3 of 100Block 4 of 100Block 5 of 100Block 6 of 100Block 7 of 100Block 8 of 100Block 9 of 100Block 10 of 100Block 11 of 100Block 12 of 100Block 13 of 100Block 14 of 100Block 15 of 100Block 16 of 100Block 17 of 100Block 18 of 100Block 19 of 100Block 20 of 100Block 21 of 100Block 22 of 100Block 23 of 100Block 24 of 100Block 25 of 100Block 26 of 100Block 27 of 100Block 28 of 100Block 29 of 100Block 30 of 100Block 31 of 100Block 32 of 100Block 33 of 100Block 34 of 100Block 35 of 100Block 36 of 100Block 37 of 100Block 38 of 100Block 39 of 100Block 40 of 100Block 41 of 100Block 42 of 100Block 43 of 100Block 44 of 100Block 45 of 100Block 46 of 100Block 47 of 100Block 48 of 100Block 49 of 100Block 50 of 100Block 51 of 100Block 52 of 100Block 53 of 100Block 54 of 100Block 55 of 100Block 56 of 100Block 57 of 100Block 58 of 100Block 59 of 100Block 60 of 100Block 61 of 100Block 62 of 100Block 63 of 100Block 64 of 100Block 65 of 100Block 66 of 100Block 67 of 100Block 68 of 100Block 69 of 100Block 70 of 100Block 71 of 100Block 72 of 100Block 73 of 100Block 74 of 100Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 100Block 2 of 100Block 3 of 100Block 4 of 100Block 5 of 100Block 6 of 100Block 7 of 100Block 8 of 100Block 9 of 100Block 10 of 100Block 11 of 100Block 12 of 100Block 13 of 100Block 14 of 100Block 15 of 100Block 16 of 100Block 17 of 100Block 18 of 100Block 19 of 100Block 20 of 100Block 21 of 100Block 22 of 100Block 23 of 100Block 24 of 100Block 25 of 100Block 26 of 100Block 27 of 100Block 28 of 100Block 29 of 100Block 30 of 100Block 31 of 100Block 32 of 100Block 33 of 100Block 34 of 100Block 35 of 100Block 36 of 100Block 37 of 100Block 38 of 100Block 39 of 100Block 40 of 100Block 41 of 100Block 42 of 100Block 43 of 100Block 44 of 100Block 45 of 100Block 46 of 100Block 47 of 100Block 48 of 100Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Block 4 of 4Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 4Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 2Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Block 4 of 4Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 2Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 2Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 33Block 2 of 33Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 13Block 2 of 13Block 3 of 13Block 4 of 13Block 5 of 13Block 6 of 13Block 7 of 13Block 8 of 13Block 9 of 13Block 10 of 13Block 11 of 13Block 12 of 13Block 13 of 13Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 13Block 2 of 13Block 3 of 13Block 4 of 13Block 5 of 13Block 6 of 13Block 7 of 13Block 8 of 13Block 9 of 13Block 10 of 13Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 13Block 2 of 13Block 3 of 13Block 4 of 13Block 5 of 13Block 6 of 13Block 7 of 13Block 8 of 13Block 9 of 13Block 10 of 13Block 11 of 13Block 12 of 13Block 13 of 13Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 13Block 2 of 13Block 3 of 13Block 4 of 13Block 5 of 13Block 6 of 13Block 7 of 13Block 8 of 13Block 9 of 13Block 10 of 13Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 6Block 2 of 6Block 3 of 6Block 4 of 6Block 5 of 6Block 6 of 6Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 6Block 2 of 6Block 3 of 6Block 4 of 6Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 6Block 2 of 6Block 3 of 6Block 4 of 6Block 5 of 6Block 6 of 6Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 6Block 2 of 6Block 3 of 6Block 4 of 6Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 13Block 2 of 13Block 3 of 13Block 4 of 13Block 5 of 13Block 6 of 13Block 7 of 13Block 8 of 13Block 9 of 13Block 10 of 13Block 11 of 13Block 12 of 13Block 13 of 13Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 13Block 2 of 13Block 3 of 13Block 4 of 13Block 5 of 13Block 6 of 13Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 13Block 2 of 13Block 3 of 13Block 4 of 13Block 5 of 13Block 6 of 13Block 7 of 13Block 8 of 13Block 9 of 13Block 10 of 13Block 11 of 13Block 12 of 13Block 13 of 13Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 13Block 2 of 13Block 3 of 13Block 4 of 13Block 5 of 13Block 6 of 13Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 6Block 2 of 6Block 3 of 6Block 4 of 6Block 5 of 6Block 6 of 6Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 6Block 2 of 6Block 3 of 6Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 6Block 2 of 6Block 3 of 6Block 4 of 6Block 5 of 6Block 6 of 6Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 6Block 2 of 6Block 3 of 6Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 500Block 2 of 500Block 3 of 500Block 4 of 500Block 5 of 500Block 6 of 500Block 7 of 500Block 8 of 500Block 9 of 500Block 10 of 500Block 11 of 500Block 12 of 500Block 13 of 500Block 14 of 500Block 15 of 500Block 16 of 500Block 17 of 500Block 17 of 500Block 18 of 500Block 19 of 500Block 20 of 500Block 21 of 500Block 22 of 500Block 23 of 500Block 24 of 500Block 25 of 500Block 26 of 500Block 27 of 500Block 28 of 500Block 29 of 500Block 30 of 500Block 31 of 500Block 32 of 500Block 33 of 500Block 34 of 500Block 35 of 500Block 36 of 500Block 37 of 500Block 38 of 500Block 39 of 500Block 40 of 500Block 41 of 500Block 42 of 500Block 43 of 500Block 44 of 500Block 45 of 500Block 46 of 500Block 47 of 500Block 48 of 500Block 49 of 500Block 50 of 500Block 51 of 500Block 52 of 500Block 53 of 500Block 53 of 500Block 54 of 500Block 55 of 500Block 56 of 500Block 57 of 500Block 58 of 500Block 59 of 500Block 60 of 500Block 61 of 500Block 62 of 500Block 63 of 500Block 64 of 500Block 65 of 500Block 66 of 500Block 67 of 500Block 68 of 500Block 69 of 500Block 70 of 500Block 71 of 500Block 72 of 500Block 73 of 500Block 74 of 500Block 75 of 500Block 76 of 500Block 77 of 500Block 78 of 500Block 79 of 500Block 80 of 500Block 81 of 500Block 82 of 500Block 83 of 500Block 84 of 500Block 85 of 500Block 86 of 500Block 87 of 500Block 88 of 500Block 89 of 500Block 90 of 500Block 91 of 500Block 92 of 500Block 93 of 500Block 94 of 500Block 95 of 500Block 96 of 500Block 97 of 500Block 98 of 500Block 99 of 500Block 100 of 500Block 101 of 500Block 102 of 500Block 103 of 500Block 104 of 500Block 105 of 500Block 106 of 500Block 107 of 500Block 108 of 500Block 109 of 500Block 110 of 500Block 111 of 500Block 112 of 500Block 113 of 500Block 114 of 500Block 115 of 500Block 116 of 500Block 117 of 500Block 118 of 500Block 119 of 500Block 120 of 500Block 121 of 500Block 122 of 500Block 123 of 500Block 124 of 500Block 125 of 500Block 126 of 500Block 127 of 500Block 128 of 500Block 129 of 500Block 130 of 500Block 131 of 500Block 132 of 500Block 133 of 500Block 134 of 500Block 135 of 500Block 136 of 500Block 137 of 500Block 138 of 500Block 139 of 500Block 140 of 500Block 141 of 500Block 142 of 500Block 143 of 500Block 144 of 500Block 145 of 500Block 146 of 500Block 147 of 500Block 148 of 500Block 149 of 500Block 150 of 500Block 151 of 500Block 152 of 500Block 153 of 500Block 154 of 500Block 155 of 500Block 156 of 500Block 157 of 500Block 158 of 500Block 159 of 500Block 160 of 500Block 161 of 500Block 162 of 500Block 163 of 500Block 164 of 500Block 165 of 500Block 166 of 500Block 167 of 500Block 168 of 500Block 169 of 500Block 170 of 500Block 171 of 500Block 172 of 500Block 173 of 500Block 174 of 500Block 175 of 500Block 176 of 500Block 177 of 500Block 178 of 500Block 179 of 500Block 180 of 500Block 181 of 500Block 182 of 500Block 183 of 500Block 184 of 500Block 185 of 500Block 185 of 500Block 186 of 500Block 187 of 500Block 188 of 500Block 189 of 500Block 190 of 500Block 191 of 500Block 192 of 500Block 193 of 500Block 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500Block 257 of 500Block 258 of 500Block 259 of 500Block 260 of 500Block 261 of 500Block 262 of 500Block 263 of 500Block 264 of 500Block 265 of 500Block 266 of 500Block 267 of 500Block 268 of 500Block 268 of 500Block 269 of 500Block 270 of 500Block 271 of 500Block 272 of 500Block 273 of 500Block 274 of 500Block 275 of 500Block 276 of 500Block 277 of 500Block 278 of 500Block 279 of 500Block 280 of 500Block 281 of 500Block 282 of 500Block 283 of 500Block 284 of 500Block 285 of 500Block 286 of 500Block 287 of 500Block 288 of 500Block 289 of 500Block 290 of 500Block 291 of 500Block 292 of 500Block 293 of 500Block 294 of 500Block 295 of 500Block 296 of 500Block 297 of 500Block 298 of 500Block 299 of 500Block 300 of 500Block 301 of 500Block 302 of 500Block 303 of 500Block 304 of 500Block 305 of 500Block 306 of 500Block 307 of 500Block 308 of 500Block 309 of 500Block 310 of 500Block 311 of 500Block 312 of 500Block 313 of 500Block 314 of 500Block 315 of 500Block 316 of 500Block 317 of 500Block 318 of 500Block 319 of 500Block 320 of 500Block 321 of 500Block 322 of 500Block 323 of 500Block 324 of 500Block 325 of 500Block 326 of 500Block 327 of 500Block 328 of 500Block 329 of 500Block 330 of 500Block 331 of 500Block 332 of 500Block 333 of 500Block 334 of 500Block 335 of 500Block 336 of 500Block 337 of 500Block 338 of 500Block 339 of 500Block 340 of 500Block 341 of 500Block 342 of 500Block 343 of 500Block 344 of 500Block 345 of 500Block 346 of 500Block 347 of 500Block 348 of 500Block 349 of 500Block 350 of 500Block 351 of 500Block 352 of 500Block 353 of 500Block 354 of 500Block 355 of 500Block 355 of 500Block 356 of 500Block 357 of 500Block 358 of 500Block 359 of 500Block 360 of 500Block 361 of 500Block 362 of 500Block 363 of 500Block 364 of 500Block 365 of 500Block 366 of 500Block 367 of 500Block 368 of 500Block 369 of 500Block 370 of 500Block 371 of 500Block 372 of 500Block 373 of 500Block 374 of 500Block 375 of 500Block 376 of 500Block 377 of 500Block 378 of 500Block 379 of 500Block 380 of 500Block 381 of 500Block 382 of 500Block 383 of 500Block 384 of 500Block 385 of 500Block 386 of 500Block 387 of 500Block 388 of 500Block 389 of 500Block 390 of 500Block 391 of 500Block 392 of 500Block 393 of 500Block 394 of 500Block 395 of 500Block 396 of 500Block 397 of 500Block 398 of 500Block 399 of 500Block 400 of 500Block 401 of 500Block 402 of 500Block 403 of 500Block 404 of 500Block 405 of 500Block 406 of 500Block 407 of 500Block 408 of 500Block 409 of 500Block 410 of 500Block 411 of 500Block 412 of 500Block 413 of 500Block 414 of 500Block 415 of 500Block 416 of 500Block 417 of 500Block 418 of 500Block 419 of 500Block 420 of 500Block 421 of 500Block 422 of 500Block 423 of 500Block 424 of 500Block 425 of 500Block 426 of 500Block 427 of 500Block 428 of 500Block 429 of 500Block 430 of 500Block 431 of 500Block 432 of 500Block 433 of 500Block 434 of 500Block 435 of 500Block 436 of 500Block 437 of 500Block 438 of 500Block 439 of 500Block 440 of 500Block 441 of 500Block 442 of 500Block 443 of 500Block 444 of 500Block 445 of 500Block 446 of 500Block 447 of 500Block 448 of 500Block 449 of 500Block 450 of 500Block 451 of 500Block 452 of 500Block 453 of 500Block 454 of 500Block 455 of 500Block 456 of 500Block 457 of 500Block 458 of 500Block 459 of 500Block 460 of 500Block 461 of 500Block 462 of 500Block 463 of 500Block 464 of 500Block 465 of 500Block 466 of 500Block 467 of 500Block 468 of 500Block 469 of 500Block 470 of 500Block 471 of 500Block 472 of 500Block 473 of 500Block 474 of 500Block 475 of 500Block 476 of 500Block 477 of 500Block 478 of 500Block 479 of 500Block 480 of 500Block 481 of 500Block 482 of 500Block 483 of 500Block 484 of 500Block 485 of 500Block 486 of 500Block 487 of 500Block 488 of 500Block 489 of 500Block 490 of 500Block 491 of 500Block 492 of 500Block 493 of 500Block 494 of 500Block 495 of 500Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 500Block 2 of 500Block 3 of 500Block 4 of 500Block 5 of 500Block 6 of 500Block 7 of 500Block 8 of 500Block 9 of 500Block 10 of 500Block 11 of 500Block 12 of 500Block 13 of 500Block 14 of 500Block 15 of 500Block 16 of 500Block 17 of 500Block 17 of 500Block 18 of 500Block 19 of 500Block 20 of 500Block 21 of 500Block 22 of 500Block 23 of 500Block 24 of 500Block 25 of 500Block 26 of 500Block 27 of 500Block 28 of 500Block 29 of 500Block 30 of 500Block 31 of 500Block 32 of 500Block 33 of 500Block 34 of 500Block 35 of 500Block 36 of 500Block 37 of 500Block 38 of 500Block 39 of 500Block 40 of 500Block 41 of 500Block 42 of 500Block 43 of 500Block 44 of 500Block 45 of 500Block 46 of 500Block 47 of 500Block 48 of 500Block 49 of 500Block 50 of 500Block 51 of 500Block 52 of 500Block 53 of 500Block 53 of 500Block 54 of 500Block 55 of 500Block 56 of 500Block 57 of 500Block 58 of 500Block 59 of 500Block 60 of 500Block 61 of 500Block 62 of 500Block 63 of 500Block 64 of 500Block 65 of 500Block 66 of 500Block 67 of 500Block 68 of 500Block 69 of 500Block 70 of 500Block 71 of 500Block 72 of 500Block 73 of 500Block 74 of 500Block 75 of 500Block 76 of 500Block 77 of 500Block 78 of 500Block 79 of 500Block 80 of 500Block 81 of 500Block 82 of 500Block 83 of 500Block 84 of 500Block 85 of 500Block 86 of 500Block 87 of 500Block 88 of 500Block 89 of 500Block 90 of 500Block 91 of 500Block 92 of 500Block 93 of 500Block 94 of 500Block 95 of 500Block 96 of 500Block 97 of 500Block 98 of 500Block 99 of 500Block 100 of 500Block 101 of 500Block 102 of 500Block 103 of 500Block 104 of 500Block 105 of 500Block 106 of 500Block 107 of 500Block 108 of 500Block 109 of 500Block 110 of 500Block 111 of 500Block 112 of 500Block 113 of 500Block 114 of 500Block 115 of 500Block 116 of 500Block 117 of 500Block 118 of 500Block 119 of 500Block 120 of 500Block 121 of 500Block 122 of 500Block 123 of 500Block 124 of 500Block 125 of 500Block 126 of 500Block 127 of 500Block 128 of 500Block 129 of 500Block 130 of 500Block 131 of 500Block 132 of 500Block 133 of 500Block 134 of 500Block 135 of 500Block 136 of 500Block 137 of 500Block 138 of 500Block 139 of 500Block 140 of 500Block 141 of 500Block 142 of 500Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 500Block 2 of 500Block 3 of 500Block 4 of 500Block 5 of 500Block 6 of 500Block 7 of 500Block 8 of 500Block 9 of 500Block 10 of 500Block 11 of 500Block 12 of 500Block 13 of 500Block 14 of 500Block 15 of 500Block 16 of 500Block 17 of 500Block 17 of 500Block 18 of 500Block 19 of 500Block 20 of 500Block 21 of 500Block 22 of 500Block 23 of 500Block 24 of 500Block 25 of 500Block 26 of 500Block 27 of 500Block 28 of 500Block 29 of 500Block 30 of 500Block 31 of 500Block 32 of 500Block 33 of 500Block 34 of 500Block 35 of 500Block 36 of 500Block 37 of 500Block 38 of 500Block 39 of 500Block 40 of 500Block 41 of 500Block 42 of 500Block 43 of 500Block 44 of 500Block 45 of 500Block 46 of 500Block 47 of 500Block 48 of 500Block 49 of 500Block 50 of 500Block 51 of 500Block 52 of 500Block 53 of 500Block 53 of 500Block 54 of 500Block 55 of 500Block 56 of 500Block 57 of 500Block 58 of 500Block 59 of 500Block 60 of 500Block 61 of 500Block 62 of 500Block 63 of 500Block 64 of 500Block 65 of 500Block 66 of 500Block 67 of 500Block 68 of 500Block 69 of 500Block 70 of 500Block 71 of 500Block 72 of 500Block 73 of 500Block 74 of 500Block 75 of 500Block 76 of 500Block 77 of 500Block 78 of 500Block 79 of 500Block 80 of 500Block 81 of 500Block 82 of 500Block 83 of 500Block 84 of 500Block 85 of 500Block 86 of 500Block 87 of 500Block 88 of 500Block 89 of 500Block 90 of 500Block 91 of 500Block 92 of 500Block 93 of 500Block 94 of 500Block 95 of 500Block 96 of 500Block 97 of 500Block 98 of 500Block 99 of 500Block 100 of 500Block 101 of 500Block 102 of 500Block 103 of 500Block 104 of 500Block 105 of 500Block 106 of 500Block 107 of 500Block 108 of 500Block 109 of 500Block 110 of 500Block 111 of 500Block 112 of 500Block 113 of 500Block 114 of 500Block 115 of 500Block 116 of 500Block 117 of 500Block 118 of 500Block 119 of 500Block 120 of 500Block 121 of 500Block 122 of 500Block 123 of 500Block 124 of 500Block 125 of 500Block 126 of 500Block 127 of 500Block 128 of 500Block 129 of 500Block 130 of 500Block 131 of 500Block 132 of 500Block 133 of 500Block 134 of 500Block 135 of 500Block 136 of 500Block 137 of 500Block 138 of 500Block 139 of 500Block 140 of 500Block 141 of 500Block 142 of 500Block 143 of 500Block 144 of 500Block 145 of 500Block 146 of 500Block 147 of 500Block 148 of 500Block 149 of 500Block 150 of 500Block 151 of 500Block 152 of 500Block 153 of 500Block 154 of 500Block 155 of 500Block 156 of 500Block 157 of 500Block 158 of 500Block 159 of 500Block 160 of 500Block 161 of 500Block 162 of 500Block 163 of 500Block 164 of 500Block 165 of 500Block 166 of 500Block 167 of 500Block 168 of 500Block 169 of 500Block 170 of 500Block 171 of 500Block 172 of 500Block 173 of 500Block 174 of 500Block 175 of 500Block 176 of 500Block 177 of 500Block 178 of 500Block 179 of 500Block 180 of 500Block 181 of 500Block 182 of 500Block 183 of 500Block 184 of 500Block 185 of 500Block 185 of 500Block 186 of 500Block 187 of 500Block 188 of 500Block 189 of 500Block 190 of 500Block 191 of 500Block 192 of 500Block 193 of 500Block 194 of 500Block 195 of 500Block 196 of 500Block 197 of 500Block 198 of 500Block 199 of 500Block 200 of 500Block 201 of 500Block 202 of 500Block 203 of 500Block 204 of 500Block 205 of 500Block 206 of 500Block 207 of 500Block 208 of 500Block 209 of 500Block 210 of 500Block 211 of 500Block 212 of 500Block 213 of 500Block 214 of 500Block 215 of 500Block 216 of 500Block 217 of 500Block 218 of 500Block 219 of 500Block 220 of 500Block 221 of 500Block 222 of 500Block 223 of 500Block 224 of 500Block 225 of 500Block 226 of 500Block 227 of 500Block 228 of 500Block 229 of 500Block 230 of 500Block 231 of 500Block 232 of 500Block 233 of 500Block 234 of 500Block 235 of 500Block 236 of 500Block 237 of 500Block 238 of 500Block 239 of 500Block 240 of 500Block 241 of 500Block 242 of 500Block 243 of 500Block 244 of 500Block 245 of 500Block 246 of 500Block 247 of 500Block 248 of 500Block 249 of 500Block 250 of 500Block 251 of 500Block 252 of 500Block 253 of 500Block 254 of 500Block 255 of 500Block 256 of 500Block 257 of 500Block 258 of 500Block 259 of 500Block 260 of 500Block 261 of 500Block 262 of 500Block 263 of 500Block 264 of 500Block 265 of 500Block 266 of 500Block 267 of 500Block 268 of 500Block 268 of 500Block 269 of 500Block 270 of 500Block 271 of 500Block 272 of 500Block 273 of 500Block 274 of 500Block 275 of 500Block 276 of 500Block 277 of 500Block 278 of 500Block 279 of 500Block 280 of 500Block 281 of 500Block 282 of 500Block 283 of 500Block 284 of 500Block 285 of 500Block 286 of 500Block 287 of 500Block 288 of 500Block 289 of 500Block 290 of 500Block 291 of 500Block 292 of 500Block 293 of 500Block 294 of 500Block 295 of 500Block 296 of 500Block 297 of 500Block 298 of 500Block 299 of 500Block 300 of 500Block 301 of 500Block 302 of 500Block 303 of 500Block 304 of 500Block 305 of 500Block 306 of 500Block 307 of 500Block 308 of 500Block 309 of 500Block 310 of 500Block 311 of 500Block 312 of 500Block 313 of 500Block 314 of 500Block 315 of 500Block 316 of 500Block 317 of 500Block 318 of 500Block 319 of 500Block 320 of 500Block 321 of 500Block 322 of 500Block 323 of 500Block 324 of 500Block 325 of 500Block 326 of 500Block 327 of 500Block 328 of 500Block 329 of 500Block 330 of 500Block 331 of 500Block 332 of 500Block 333 of 500Block 334 of 500Block 335 of 500Block 336 of 500Block 337 of 500Block 338 of 500Block 339 of 500Block 340 of 500Block 341 of 500Block 342 of 500Block 343 of 500Block 344 of 500Block 345 of 500Block 346 of 500Block 347 of 500Block 348 of 500Block 349 of 500Block 350 of 500Block 351 of 500Block 352 of 500Block 353 of 500Block 354 of 500Block 355 of 500Block 355 of 500Block 356 of 500Block 357 of 500Block 358 of 500Block 359 of 500Block 360 of 500Block 361 of 500Block 362 of 500Block 363 of 500Block 364 of 500Block 365 of 500Block 366 of 500Block 367 of 500Block 368 of 500Block 369 of 500Block 370 of 500Block 371 of 500Block 372 of 500Block 373 of 500Block 374 of 500Block 375 of 500Block 376 of 500Block 377 of 500Block 378 of 500Block 379 of 500Block 380 of 500Block 381 of 500Block 382 of 500Block 383 of 500Block 384 of 500Block 385 of 500Block 386 of 500Block 387 of 500Block 388 of 500Block 389 of 500Block 390 of 500Block 391 of 500Block 392 of 500Block 393 of 500Block 394 of 500Block 395 of 500Block 396 of 500Block 397 of 500Block 398 of 500Block 399 of 500Block 400 of 500Block 401 of 500Block 402 of 500Block 403 of 500Block 404 of 500Block 405 of 500Block 406 of 500Block 407 of 500Block 408 of 500Block 409 of 500Block 410 of 500Block 411 of 500Block 412 of 500Block 413 of 500Block 414 of 500Block 415 of 500Block 416 of 500Block 417 of 500Block 418 of 500Block 419 of 500Block 420 of 500Block 421 of 500Block 422 of 500Block 423 of 500Block 424 of 500Block 425 of 500Block 426 of 500Block 427 of 500Block 428 of 500Block 429 of 500Block 430 of 500Block 431 of 500Block 432 of 500Block 433 of 500Block 434 of 500Block 435 of 500Block 436 of 500Block 437 of 500Block 438 of 500Block 439 of 500Block 440 of 500Block 441 of 500Block 442 of 500Block 443 of 500Block 444 of 500Block 445 of 500Block 446 of 500Block 447 of 500Block 448 of 500Block 449 of 500Block 450 of 500Block 451 of 500Block 452 of 500Block 453 of 500Block 454 of 500Block 455 of 500Block 456 of 500Block 457 of 500Block 458 of 500Block 459 of 500Block 460 of 500Block 461 of 500Block 462 of 500Block 463 of 500Block 464 of 500Block 465 of 500Block 466 of 500Block 467 of 500Block 468 of 500Block 469 of 500Block 470 of 500Block 471 of 500Block 472 of 500Block 473 of 500Block 474 of 500Block 475 of 500Block 476 of 500Block 477 of 500Block 478 of 500Block 479 of 500Block 480 of 500Block 481 of 500Block 482 of 500Block 483 of 500Block 484 of 500Block 485 of 500Block 486 of 500Block 487 of 500Block 488 of 500Block 489 of 500Block 490 of 500Block 491 of 500Block 492 of 500Block 493 of 500Block 494 of 500Block 495 of 500Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 500Block 2 of 500Block 3 of 500Block 4 of 500Block 5 of 500Block 6 of 500Block 7 of 500Block 8 of 500Block 9 of 500Block 10 of 500Block 11 of 500Block 12 of 500Block 13 of 500Block 14 of 500Block 15 of 500Block 16 of 500Block 17 of 500Block 17 of 500Block 18 of 500Block 19 of 500Block 20 of 500Block 21 of 500Block 22 of 500Block 23 of 500Block 24 of 500Block 25 of 500Block 26 of 500Block 27 of 500Block 28 of 500Block 29 of 500Block 30 of 500Block 31 of 500Block 32 of 500Block 33 of 500Block 34 of 500Block 35 of 500Block 36 of 500Block 37 of 500Block 38 of 500Block 39 of 500Block 40 of 500Block 41 of 500Block 42 of 500Block 43 of 500Block 44 of 500Block 45 of 500Block 46 of 500Block 47 of 500Block 48 of 500Block 49 of 500Block 50 of 500Block 51 of 500Block 52 of 500Block 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500Block 490 of 500Block 491 of 500Block 492 of 500Block 493 of 500Block 494 of 500Block 495 of 500Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 500Block 2 of 500Block 3 of 500Block 4 of 500Block 5 of 500Block 6 of 500Block 7 of 500Block 8 of 500Block 9 of 500Block 10 of 500Block 11 of 500Block 12 of 500Block 13 of 500Block 14 of 500Block 15 of 500Block 16 of 500Block 17 of 500Block 17 of 500Block 18 of 500Block 19 of 500Block 20 of 500Block 21 of 500Block 22 of 500Block 23 of 500Block 24 of 500Block 25 of 500Block 26 of 500Block 27 of 500Block 28 of 500Block 29 of 500Block 30 of 500Block 31 of 500Block 32 of 500Block 33 of 500Block 34 of 500Block 35 of 500Block 36 of 500Block 37 of 500Block 38 of 500Block 39 of 500Block 40 of 500Block 41 of 500Block 42 of 500Block 43 of 500Block 44 of 500Block 45 of 500Block 46 of 500Block 47 of 500Block 48 of 500Block 49 of 500Block 50 of 500Block 51 of 500Block 52 of 500Block 53 of 500Block 53 of 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500Block 119 of 500Block 120 of 500Block 121 of 500Block 122 of 500Block 123 of 500Block 124 of 500Block 125 of 500Block 126 of 500Block 127 of 500Block 128 of 500Block 129 of 500Block 130 of 500Block 131 of 500Block 132 of 500Block 133 of 500Block 134 of 500Block 135 of 500Block 136 of 500Block 137 of 500Block 138 of 500Block 139 of 500Block 140 of 500Block 141 of 500Block 142 of 500Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 500Block 2 of 500Block 3 of 500Block 4 of 500Block 5 of 500Block 6 of 500Block 7 of 500Block 8 of 500Block 9 of 500Block 10 of 500Block 11 of 500Block 12 of 500Block 13 of 500Block 14 of 500Block 15 of 500Block 16 of 500Block 17 of 500Block 17 of 500Block 18 of 500Block 19 of 500Block 20 of 500Block 21 of 500Block 22 of 500Block 23 of 500Block 24 of 500Block 25 of 500Block 26 of 500Block 27 of 500Block 28 of 500Block 29 of 500Block 30 of 500Block 31 of 500Block 32 of 500Block 33 of 500Block 34 of 500Block 35 of 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500Block 411 of 500Block 412 of 500Block 413 of 500Block 414 of 500Block 415 of 500Block 416 of 500Block 417 of 500Block 418 of 500Block 419 of 500Block 420 of 500Block 421 of 500Block 422 of 500Block 423 of 500Block 424 of 500Block 425 of 500Block 426 of 500Block 427 of 500Block 428 of 500Block 429 of 500Block 430 of 500Block 431 of 500Block 432 of 500Block 433 of 500Block 434 of 500Block 435 of 500Block 436 of 500Block 437 of 500Block 438 of 500Block 439 of 500Block 440 of 500Block 441 of 500Block 442 of 500Block 443 of 500Block 444 of 500Block 445 of 500Block 446 of 500Block 447 of 500Block 448 of 500Block 449 of 500Block 450 of 500Block 451 of 500Block 452 of 500Block 453 of 500Block 454 of 500Block 455 of 500Block 456 of 500Block 457 of 500Block 458 of 500Block 459 of 500Block 460 of 500Block 461 of 500Block 462 of 500Block 463 of 500Block 464 of 500Block 465 of 500Block 466 of 500Block 467 of 500Block 468 of 500Block 469 of 500Block 470 of 500Block 471 of 500Block 472 of 500Block 473 of 500Block 474 of 500Block 475 of 500Block 476 of 500Block 477 of 500Block 478 of 500Block 479 of 500Block 480 of 500Block 481 of 500Block 482 of 500Block 483 of 500Block 484 of 500Block 485 of 500Block 486 of 500Block 487 of 500Block 488 of 500Block 489 of 500Block 490 of 500Block 491 of 500Block 492 of 500Block 493 of 500Block 494 of 500Block 495 of 500adding variables: quality, X, YClean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a402cc98dbd' (67.1K)    # of fragments: 35    save to '/private/tmp/RtmperfYBE/file17a402cc98dbd.tmp'    rename '/private/tmp/RtmperfYBE/file17a402cc98dbd.tmp' (66.9K, reduced: 216B)    # of fragments: 17Fri Dec 12 05:43:07 2025begin convertNcdfGds ...Fri Dec 12 05:43:07 2025Creating GDS file ...Fri Dec 12 05:43:07 2025Adding sample data...Fri Dec 12 05:43:07 2025end convertNcdfGds.Fri Dec 12 05:43:07 2025begin checkNcdfGds ...The numbers of samples are equalThe numbers of snps are equal.Fri Dec 12 05:43:07 2025Checking in the sample order ...OK!!!Fri Dec 12 05:43:07 2025begin checkNcdfGds ...The numbers of samples are equalThe numbers of snps are equal.Fri Dec 12 05:43:08 2025Checking in the sample order ...The 1th sample error!Fri Dec 12 05:43:08 2025begin convertGdsNcdf ...Fri Dec 12 05:43:08 2025Creating NetCDF file ...Fri Dec 12 05:43:08 2025Adding sample data ...Fri Dec 12 05:43:08 2025end convertGdsNcdf.Fri Dec 12 05:43:08 2025begin convertGdsNcdf ...Fri Dec 12 05:43:08 2025Creating NetCDF file ...Fri Dec 12 05:43:08 2025Adding sample data ...Fri Dec 12 05:43:08 2025end convertGdsNcdf.SNP genotypes: 20 samples, 260 SNPsGenotype matrix is being transposed ...Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a40486c38c0' (4.3K)    # of fragments: 13    save to '/tmp/RtmperfYBE/file17a40486c38c0.tmp'    rename '/tmp/RtmperfYBE/file17a40486c38c0.tmp' (3.0K, reduced: 1.4K)    # of fragments: 11Fri Dec 12 05:43:08 2025begin convertGdsNcdf ...Fri Dec 12 05:43:08 2025Creating NetCDF file ...Fri Dec 12 05:43:08 2025Adding sample data ...Fri Dec 12 05:43:08 2025end convertGdsNcdf.Fri Dec 12 05:43:08 2025begin convertNcdfGds ...Fri Dec 12 05:43:08 2025Creating GDS file ...Fri Dec 12 05:43:08 2025Adding sample data...Fri Dec 12 05:43:08 2025end convertNcdfGds.Fri Dec 12 05:43:08 2025begin convertNcdfGds ...Fri Dec 12 05:43:08 2025Creating GDS file ...Fri Dec 12 05:43:08 2025Adding sample data...Fri Dec 12 05:43:08 2025end convertNcdfGds.Fri Dec 12 05:43:09 2025begin convertNcdfGds ...Fri Dec 12 05:43:09 2025Creating GDS file ...Fri Dec 12 05:43:09 2025Adding sample data...Fri Dec 12 05:43:09 2025end convertNcdfGds.Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401e495be6' (88.4K)    # of fragments: 31    save to '/private/tmp/RtmperfYBE/file17a401e495be6.tmp'    rename '/private/tmp/RtmperfYBE/file17a401e495be6.tmp' (88.3K, reduced: 192B)    # of fragments: 15adding variables: genotypeClean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a40bd9effd' (25.3K)    # of fragments: 26    save to '/private/tmp/RtmperfYBE/file17a40bd9effd.tmp'    rename '/private/tmp/RtmperfYBE/file17a40bd9effd.tmp' (25.1K, reduced: 156B)    # of fragments: 13adding variables: genotypeadding variables: genotypeClean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a402e51bf8e' (28.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a402e51bf8e.tmp'    rename '/private/tmp/RtmperfYBE/file17a402e51bf8e.tmp' (28.3K, reduced: 180B)    # of fragments: 15adding variables: genotypeClean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401f08a418' (27.1K)    # of fragments: 26    save to '/private/tmp/RtmperfYBE/file17a401f08a418.tmp'    rename '/private/tmp/RtmperfYBE/file17a401f08a418.tmp' (27.0K, reduced: 156B)    # of fragments: 13adding variables: genotypeadding variables: quality, X, YClean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4024fdb76' (67.1K)    # of fragments: 35    save to '/private/tmp/RtmperfYBE/file17a4024fdb76.tmp'    rename '/private/tmp/RtmperfYBE/file17a4024fdb76.tmp' (66.9K, reduced: 216B)    # of fragments: 17adding variables: quality, X, Yadding variables: genotypeClean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a406e0fdf2' (28.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a406e0fdf2.tmp'    rename '/private/tmp/RtmperfYBE/file17a406e0fdf2.tmp' (28.3K, reduced: 180B)    # of fragments: 15working on genotypegenotype - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a405c8b87e3' (2.6K)    # of fragments: 31    save to '/tmp/RtmperfYBE/file17a405c8b87e3.tmp'    rename '/tmp/RtmperfYBE/file17a405c8b87e3.tmp' (2.4K, reduced: 192B)    # of fragments: 15working on genotypegenotype - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a404c86778c' (2.6K)    # of fragments: 31    save to '/tmp/RtmperfYBE/file17a404c86778c.tmp'    rename '/tmp/RtmperfYBE/file17a404c86778c.tmp' (2.4K, reduced: 192B)    # of fragments: 15Comparing identical datasetsMatching variants on position, allelesCalculating squared correlation of allelic dosages at 20 overlapping variants in 10 duplicate sample pairsDetecting that the two datasets are counting different A alleles at 0 variantsGetting genotypes:Calculating correlation by SNPBlock 1 of 2Block 2 of 2Calculating correlation by sampleBlock 1 of 2Block 2 of 2Finished!Comparing no matching samplesComparing >1 dup pairMatching variants on position, allelesCalculating squared correlation of allelic dosages at 20 overlapping variants in 9 duplicate sample pairsDetecting that the two datasets are counting different A alleles at 0 variantsGetting genotypes:Calculating correlation by SNPBlock 1 of 1Calculating correlation by sampleBlock 1 of 1Finished!Comparing different datasetsMatching variants on position, allelesCalculating squared correlation of allelic dosages at 19 overlapping variants in 9 duplicate sample pairsDetecting that the two datasets are counting different A alleles at 1 variantsGetting genotypes:Calculating correlation by SNPBlock 1 of 1Calculating correlation by sampleBlock 1 of 1Finished!selecting genotypes from genoData1selecting genotypes from genoData2subject 1 out of 3, 2 replicationssubject 2 out of 3, 2 replicationssubject 3 out of 3, 2 replicationssubject 1 out of 3, 2 replicationssubject 2 out of 3, 2 replicationssubject 3 out of 3, 2 replicationssubject 1 out of 3, 2 replicationssubject 2 out of 3, 2 replicationssubject 3 out of 3, 2 replicationsCalculating allele freqency in genoData1subject 1 out of 3, 2 replicationssubject 2 out of 3, 2 replicationssubject 3 out of 3, 2 replicationssubject 1 out of 3, 2 replicationssubject 2 out of 3, 2 replicationssubject 3 out of 3, 3 replicationssubject 1 out of 3, 2 replicationssubject 2 out of 3, 2 replicationssubject 3 out of 3, 2 replicationssubject 1 out of 3, 2 replicationssubject 2 out of 3, 2 replicationssubject 3 out of 3, 3 replicationssubject 1 out of 3, 2 replicationssubject 2 out of 3, 2 replicationssubject 3 out of 3, 3 replicationssubject 1 out of 2, 2 replicationssubject 2 out of 2, 2 replicationsCalculating allele freqency in genoData1subject 1 out of 4subject 2 out of 4subject 3 out of 4subject 4 out of 4subject 1 out of 2, 3 replicationssubject 2 out of 2, 2 replicationscalculating dosage correlation by SNP, in blocks of 5,000 SNPsBlock 1 of 1subject 1 out of 2, 2 replicationssubject 2 out of 2, 2 replicationscalculating dosage correlation by SNP, in blocks of 5,000 SNPsBlock 1 of 1subject 1 out of 2, 3 replicationssubject 2 out of 2, 2 replicationscalculating dosage correlation by SNP, in blocks of 5,000 SNPsBlock 1 of 1subject 1 out of 2, 2 replicationssubject 2 out of 2, 2 replicationssubject 1 out of 2, 3 replicationssubject 2 out of 2, 2 replicationssubject 1 out of 2, 3 replicationssubject 2 out of 2, 2 replicationsBeginning Calculations...Block 1 of 1 Completed - 0.0008512 secsBeginning Calculations...Block 1 of 1 Completed - 0.000772 secsBeginning Calculations...Block 1 of 1 Completed - 7e-04 secsBeginning Calculations...Block 1 of 1 Completed - 0.002571 secsBeginning Calculations...Block 1 of 1 Completed - 0.0007868 secsBeginning Calculations...Block 1 of 1 Completed - 0.001697 secsworking on genotypegenotype - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4065340eea' (2.3K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a4065340eea.tmp'    rename '/tmp/RtmperfYBE/file17a4065340eea.tmp' (2.1K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over samplesAll variables match.working on genotypegenotype - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4078e420a0' (2.3K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a4078e420a0.tmp'    rename '/tmp/RtmperfYBE/file17a4078e420a0.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over samplesAll variables match.working on genotypeworking on genotypeworking on genotypegenotype - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a406d03b97e' (2.3K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a406d03b97e.tmp'    rename '/tmp/RtmperfYBE/file17a406d03b97e.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over samplesAll variables match.working on genotypegenotype - looping over samplesworking on genotypegenotype - looping over samplesAll variables match.working on genotypegenotype - looping over samplesworking on genotypegenotype - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a40143a1d76' (2.3K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a40143a1d76.tmp'    rename '/tmp/RtmperfYBE/file17a40143a1d76.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over samplesworking on genotypegenotype - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a40fb0dd85' (2.3K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a40fb0dd85.tmp'    rename '/tmp/RtmperfYBE/file17a40fb0dd85.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over samplesAll variables match.working on genotypegenotype - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a40249f4ecf' (3.2K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a40249f4ecf.tmp'    rename '/tmp/RtmperfYBE/file17a40249f4ecf.tmp' (3.0K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over samplesAll variables match.working on genotypegenotype - sample 10 of 20genotype - sample 20 of 20Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4056ef0ad1' (2.5K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a4056ef0ad1.tmp'    rename '/tmp/RtmperfYBE/file17a4056ef0ad1.tmp' (2.3K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over samplesAll variables match.working on genotypegenotype - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4028fb9e6c' (2.3K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a4028fb9e6c.tmp'    rename '/tmp/RtmperfYBE/file17a4028fb9e6c.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over samplesAll variables match.working on genotypeworking on genotypegenotype - block 1 of 1Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4058fcf8df' (2.3K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a4058fcf8df.tmp'    rename '/tmp/RtmperfYBE/file17a4058fcf8df.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over snpsAll variables match.working on genotypegenotype - block 1 of 13genotype - block 2 of 13genotype - block 3 of 13genotype - block 4 of 13genotype - block 5 of 13genotype - block 6 of 13genotype - block 7 of 13genotype - block 8 of 13genotype - block 9 of 13genotype - block 10 of 13genotype - block 11 of 13genotype - block 12 of 13genotype - block 13 of 13Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a404837261d' (2.3K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a404837261d.tmp'    rename '/tmp/RtmperfYBE/file17a404837261d.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over snpsAll variables match.working on genotypegenotype - block 1 of 2genotype - block 2 of 2Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a401ca75ef5' (2.3K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a401ca75ef5.tmp'    rename '/tmp/RtmperfYBE/file17a401ca75ef5.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over snpsAll variables match.working on genotypegenotype - block 1 of 260genotype - block 2 of 260genotype - block 3 of 260genotype - block 4 of 260genotype - block 5 of 260genotype - block 6 of 260genotype - block 7 of 260genotype - block 8 of 260genotype - block 9 of 260genotype - block 10 of 260genotype - block 11 of 260genotype - block 12 of 260genotype - block 13 of 260genotype - block 14 of 260genotype - block 15 of 260genotype - block 16 of 260genotype - block 17 of 260genotype - block 18 of 260genotype - block 19 of 260genotype - block 20 of 260genotype - block 21 of 260genotype - block 22 of 260genotype - block 23 of 260genotype - block 24 of 260genotype - block 25 of 260genotype - block 26 of 260genotype - block 27 of 260genotype - block 28 of 260genotype - block 29 of 260genotype - block 30 of 260genotype - block 31 of 260genotype - block 32 of 260genotype - block 33 of 260genotype - block 34 of 260genotype - block 35 of 260genotype - block 36 of 260genotype - block 37 of 260genotype - block 38 of 260genotype - block 39 of 260genotype - block 40 of 260genotype - block 41 of 260genotype - block 42 of 260genotype - block 43 of 260genotype - block 44 of 260genotype - block 45 of 260genotype - block 46 of 260genotype - block 47 of 260genotype - block 48 of 260genotype - block 49 of 260genotype - block 50 of 260genotype - block 51 of 260genotype - block 52 of 260genotype - block 53 of 260genotype - block 54 of 260genotype - block 55 of 260genotype - block 56 of 260genotype - block 57 of 260genotype - block 58 of 260genotype - block 59 of 260genotype - block 60 of 260genotype - block 61 of 260genotype - block 62 of 260genotype - block 63 of 260genotype - block 64 of 260genotype - block 65 of 260genotype - block 66 of 260genotype - block 67 of 260genotype - block 68 of 260genotype - block 69 of 260genotype - block 70 of 260genotype - block 71 of 260genotype - block 72 of 260genotype - block 73 of 260genotype - block 74 of 260genotype - block 75 of 260genotype - block 76 of 260genotype - block 77 of 260genotype - block 78 of 260genotype - block 79 of 260genotype - block 80 of 260genotype - block 81 of 260genotype - block 82 of 260genotype - block 83 of 260genotype - block 84 of 260genotype - block 85 of 260genotype - block 86 of 260genotype - block 87 of 260genotype - block 88 of 260genotype - block 89 of 260genotype - block 90 of 260genotype - block 91 of 260genotype - block 92 of 260genotype - block 93 of 260genotype - block 94 of 260genotype - block 95 of 260genotype - block 96 of 260genotype - block 97 of 260genotype - block 98 of 260genotype - block 99 of 260genotype - block 100 of 260genotype - block 101 of 260genotype - block 102 of 260genotype - block 103 of 260genotype - block 104 of 260genotype - block 105 of 260genotype - block 106 of 260genotype - block 107 of 260genotype - block 108 of 260genotype - block 109 of 260genotype - block 110 of 260genotype - block 111 of 260genotype - block 112 of 260genotype - block 113 of 260genotype - block 114 of 260genotype - block 115 of 260genotype - block 116 of 260genotype - block 117 of 260genotype - block 118 of 260genotype - block 119 of 260genotype - block 120 of 260genotype - block 121 of 260genotype - block 122 of 260genotype - block 123 of 260genotype - block 124 of 260genotype - block 125 of 260genotype - block 126 of 260genotype - block 127 of 260genotype - block 128 of 260genotype - block 129 of 260genotype - block 130 of 260genotype - block 131 of 260genotype - block 132 of 260genotype - block 133 of 260genotype - block 134 of 260genotype - block 135 of 260genotype - block 136 of 260genotype - block 137 of 260genotype - block 138 of 260genotype - block 139 of 260genotype - block 140 of 260genotype - block 141 of 260genotype - block 142 of 260genotype - block 143 of 260genotype - block 144 of 260genotype - block 145 of 260genotype - block 146 of 260genotype - block 147 of 260genotype - block 148 of 260genotype - block 149 of 260genotype - block 150 of 260genotype - block 151 of 260genotype - block 152 of 260genotype - block 153 of 260genotype - block 154 of 260genotype - block 155 of 260genotype - block 156 of 260genotype - block 157 of 260genotype - block 158 of 260genotype - block 159 of 260genotype - block 160 of 260genotype - block 161 of 260genotype - block 162 of 260genotype - block 163 of 260genotype - block 164 of 260genotype - block 165 of 260genotype - block 166 of 260genotype - block 167 of 260genotype - block 168 of 260genotype - block 169 of 260genotype - block 170 of 260genotype - block 171 of 260genotype - block 172 of 260genotype - block 173 of 260genotype - block 174 of 260genotype - block 175 of 260genotype - block 176 of 260genotype - block 177 of 260genotype - block 178 of 260genotype - block 179 of 260genotype - block 180 of 260genotype - block 181 of 260genotype - block 182 of 260genotype - block 183 of 260genotype - block 184 of 260genotype - block 185 of 260genotype - block 186 of 260genotype - block 187 of 260genotype - block 188 of 260genotype - block 189 of 260genotype - block 190 of 260genotype - block 191 of 260genotype - block 192 of 260genotype - block 193 of 260genotype - block 194 of 260genotype - block 195 of 260genotype - block 196 of 260genotype - block 197 of 260genotype - block 198 of 260genotype - block 199 of 260genotype - block 200 of 260genotype - block 201 of 260genotype - block 202 of 260genotype - block 203 of 260genotype - block 204 of 260genotype - block 205 of 260genotype - block 206 of 260genotype - block 207 of 260genotype - block 208 of 260genotype - block 209 of 260genotype - block 210 of 260genotype - block 211 of 260genotype - block 212 of 260genotype - block 213 of 260genotype - block 214 of 260genotype - block 215 of 260genotype - block 216 of 260genotype - block 217 of 260genotype - block 218 of 260genotype - block 219 of 260genotype - block 220 of 260genotype - block 221 of 260genotype - block 222 of 260genotype - block 223 of 260genotype - block 224 of 260genotype - block 225 of 260genotype - block 226 of 260genotype - block 227 of 260genotype - block 228 of 260genotype - block 229 of 260genotype - block 230 of 260genotype - block 231 of 260genotype - block 232 of 260genotype - block 233 of 260genotype - block 234 of 260genotype - block 235 of 260genotype - block 236 of 260genotype - block 237 of 260genotype - block 238 of 260genotype - block 239 of 260genotype - block 240 of 260genotype - block 241 of 260genotype - block 242 of 260genotype - block 243 of 260genotype - block 244 of 260genotype - block 245 of 260genotype - block 246 of 260genotype - block 247 of 260genotype - block 248 of 260genotype - block 249 of 260genotype - block 250 of 260genotype - block 251 of 260genotype - block 252 of 260genotype - block 253 of 260genotype - block 254 of 260genotype - block 255 of 260genotype - block 256 of 260genotype - block 257 of 260genotype - block 258 of 260genotype - block 259 of 260genotype - block 260 of 260Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a40304b3585' (2.3K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a40304b3585.tmp'    rename '/tmp/RtmperfYBE/file17a40304b3585.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over snpsAll variables match.working on genotypegenotype - block 1 of 1Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4019a6c788' (3.2K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a4019a6c788.tmp'    rename '/tmp/RtmperfYBE/file17a4019a6c788.tmp' (3.0K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over snpsAll variables match.working on genotypegenotype - block 1 of 1Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a401475bee0' (2.5K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a401475bee0.tmp'    rename '/tmp/RtmperfYBE/file17a401475bee0.tmp' (2.3K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over snpsAll variables match.working on genotypegenotype - block 1 of 11genotype - block 2 of 11genotype - block 3 of 11genotype - block 4 of 11genotype - block 5 of 11genotype - block 6 of 11genotype - block 7 of 11genotype - block 8 of 11genotype - block 9 of 11genotype - block 10 of 11genotype - block 11 of 11Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4075a2f6ff' (2.4K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a4075a2f6ff.tmp'    rename '/tmp/RtmperfYBE/file17a4075a2f6ff.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over snpsAll variables match.working on genotypegenotype - block 1 of 1Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a401e061baf' (3.1K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a401e061baf.tmp'    rename '/tmp/RtmperfYBE/file17a401e061baf.tmp' (3.0K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over snpsAll variables match.working on genotypegenotype - block 1 of 1Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4023038d8f' (2.5K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a4023038d8f.tmp'    rename '/tmp/RtmperfYBE/file17a4023038d8f.tmp' (2.3K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over snpsAll variables match.working on genotypegenotype - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a407cccfabe' (2.4K)    # of fragments: 27    save to '/tmp/RtmperfYBE/file17a407cccfabe.tmp'    rename '/tmp/RtmperfYBE/file17a407cccfabe.tmp' (2.2K, reduced: 168B)    # of fragments: 13working on genotypegenotype - looping over samplesAll variables match.working on genotype1genotype1 - sample 10 of 10working on genotype2genotype2 - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a405e5704b2' (2.6K)    # of fragments: 32    save to '/tmp/RtmperfYBE/file17a405e5704b2.tmp'    rename '/tmp/RtmperfYBE/file17a405e5704b2.tmp' (2.4K, reduced: 204B)    # of fragments: 15working on genotype1genotype1 - looping over samplesworking on genotype2genotype2 - looping over samplesAll variables match.working on genotype1genotype1 - sample 10 of 10working on genotype2genotype2 - sample 10 of 10Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4022f57281' (4.0K)    # of fragments: 32    save to '/tmp/RtmperfYBE/file17a4022f57281.tmp'    rename '/tmp/RtmperfYBE/file17a4022f57281.tmp' (3.8K, reduced: 204B)    # of fragments: 15working on genotype1genotype1 - looping over samplesworking on genotype2genotype2 - looping over samplesAll variables match.working on genotype1genotype1 - sample 10 of 20genotype1 - sample 20 of 20working on genotype2genotype2 - sample 10 of 20genotype2 - sample 20 of 20Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4020308515' (2.9K)    # of fragments: 32    save to '/tmp/RtmperfYBE/file17a4020308515.tmp'    rename '/tmp/RtmperfYBE/file17a4020308515.tmp' (2.7K, reduced: 204B)    # of fragments: 15working on genotype1genotype1 - looping over samplesworking on genotype2genotype2 - looping over samplesAll variables match.Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 727B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 727B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 727B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 727B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 727B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4068c630cf' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp'    rename '/private/tmp/RtmperfYBE/file17a4068c630cf.tmp' (2.5K, reduced: 727B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4040728207' (2.6K)    # of fragments: 31    save to '/private/tmp/RtmperfYBE/file17a4040728207.tmp'    rename '/private/tmp/RtmperfYBE/file17a4040728207.tmp' (2.4K, reduced: 204B)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4040728207' (2.6K)    # of fragments: 31    save to '/private/tmp/RtmperfYBE/file17a4040728207.tmp'    rename '/private/tmp/RtmperfYBE/file17a4040728207.tmp' (2.4K, reduced: 204B)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4040728207' (2.6K)    # of fragments: 31    save to '/private/tmp/RtmperfYBE/file17a4040728207.tmp'    rename '/private/tmp/RtmperfYBE/file17a4040728207.tmp' (2.4K, reduced: 204B)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4040728207' (2.6K)    # of fragments: 31    save to '/private/tmp/RtmperfYBE/file17a4040728207.tmp'    rename '/private/tmp/RtmperfYBE/file17a4040728207.tmp' (2.4K, reduced: 204B)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4040728207' (2.6K)    # of fragments: 31    save to '/private/tmp/RtmperfYBE/file17a4040728207.tmp'    rename '/private/tmp/RtmperfYBE/file17a4040728207.tmp' (2.4K, reduced: 204B)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4040728207' (2.6K)    # of fragments: 31    save to '/private/tmp/RtmperfYBE/file17a4040728207.tmp'    rename '/private/tmp/RtmperfYBE/file17a4040728207.tmp' (2.4K, reduced: 204B)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405d829271' (3.2K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405d829271.tmp'    rename '/private/tmp/RtmperfYBE/file17a405d829271.tmp' (2.5K, reduced: 723B)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404ceb31a' (3.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp'    rename '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp' (2.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404ceb31a' (3.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp'    rename '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp' (2.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404ceb31a' (3.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp'    rename '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp' (2.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404ceb31a' (3.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp'    rename '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp' (2.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404ceb31a' (3.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp'    rename '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp' (2.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404ceb31a' (3.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp'    rename '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp' (2.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 100Block 2 of 100Block 3 of 100Block 4 of 100Block 5 of 100Block 6 of 100Block 7 of 100Block 8 of 100Block 9 of 100Block 10 of 100Block 11 of 100Block 12 of 100Block 13 of 100Block 14 of 100Block 15 of 100Block 16 of 100Block 17 of 100Block 18 of 100Block 19 of 100Block 20 of 100Block 21 of 100Block 22 of 100Block 23 of 100Block 24 of 100Block 25 of 100Block 26 of 100Block 27 of 100Block 28 of 100Block 29 of 100Block 30 of 100Block 31 of 100Block 32 of 100Block 33 of 100Block 34 of 100Block 35 of 100Block 36 of 100Block 37 of 100Block 38 of 100Block 39 of 100Block 40 of 100Block 41 of 100Block 42 of 100Block 43 of 100Block 44 of 100Block 45 of 100Block 46 of 100Block 47 of 100Block 48 of 100Block 49 of 100Block 50 of 100Block 51 of 100Block 52 of 100Block 53 of 100Block 54 of 100Block 55 of 100Block 56 of 100Block 57 of 100Block 58 of 100Block 59 of 100Block 60 of 100Block 61 of 100Block 62 of 100Block 63 of 100Block 64 of 100Block 65 of 100Block 66 of 100Block 67 of 100Block 68 of 100Block 69 of 100Block 70 of 100Block 71 of 100Block 72 of 100Block 73 of 100Block 74 of 100Block 75 of 100Block 76 of 100Block 77 of 100Block 78 of 100Block 79 of 100Block 80 of 100Block 81 of 100Block 82 of 100Block 83 of 100Block 84 of 100Block 85 of 100Block 86 of 100Block 87 of 100Block 88 of 100Block 89 of 100Block 90 of 100Block 91 of 100Block 92 of 100Block 93 of 100Block 94 of 100Block 95 of 100Block 96 of 100Block 97 of 100Block 98 of 100Block 99 of 100Block 100 of 100Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404ceb31a' (3.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp'    rename '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp' (2.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP file...Reading genotype file...Block 1 of 100Block 2 of 100Block 3 of 100Block 4 of 100Block 5 of 100Block 6 of 100Block 7 of 100Block 8 of 100Block 9 of 100Block 10 of 100Block 11 of 100Block 12 of 100Block 13 of 100Block 14 of 100Block 15 of 100Block 16 of 100Block 17 of 100Block 18 of 100Block 19 of 100Block 20 of 100Block 21 of 100Block 22 of 100Block 23 of 100Block 24 of 100Block 25 of 100Block 26 of 100Block 27 of 100Block 28 of 100Block 29 of 100Block 30 of 100Block 31 of 100Block 32 of 100Block 33 of 100Block 34 of 100Block 35 of 100Block 36 of 100Block 37 of 100Block 38 of 100Block 39 of 100Block 40 of 100Block 41 of 100Block 42 of 100Block 43 of 100Block 44 of 100Block 45 of 100Block 46 of 100Block 47 of 100Block 48 of 100Block 49 of 100Block 50 of 100Block 51 of 100Block 52 of 100Block 53 of 100Block 54 of 100Block 55 of 100Block 56 of 100Block 57 of 100Block 58 of 100Block 59 of 100Block 60 of 100Block 61 of 100Block 62 of 100Block 63 of 100Block 64 of 100Block 65 of 100Block 66 of 100Block 67 of 100Block 68 of 100Block 69 of 100Block 70 of 100Block 71 of 100Block 72 of 100Block 73 of 100Block 74 of 100Block 75 of 100Block 76 of 100Block 77 of 100Block 78 of 100Block 79 of 100Block 80 of 100Block 81 of 100Block 82 of 100Block 83 of 100Block 84 of 100Block 85 of 100Block 86 of 100Block 87 of 100Block 88 of 100Block 89 of 100Block 90 of 100Block 91 of 100Block 92 of 100Block 93 of 100Block 94 of 100Block 95 of 100Block 96 of 100Block 97 of 100Block 98 of 100Block 99 of 100Block 100 of 100Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404ceb31a' (3.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp'    rename '/private/tmp/RtmperfYBE/file17a404ceb31a.tmp' (2.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a407525c141' (34.7K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a407525c141.tmp'    rename '/private/tmp/RtmperfYBE/file17a407525c141.tmp' (4.9K, reduced: 29.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Block 4 of 4Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a407525c141' (34.7K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a407525c141.tmp'    rename '/private/tmp/RtmperfYBE/file17a407525c141.tmp' (4.9K, reduced: 29.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a407525c141' (34.7K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a407525c141.tmp'    rename '/private/tmp/RtmperfYBE/file17a407525c141.tmp' (4.9K, reduced: 29.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a407525c141' (34.7K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a407525c141.tmp'    rename '/private/tmp/RtmperfYBE/file17a407525c141.tmp' (4.9K, reduced: 29.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Block 4 of 4Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a407525c141' (34.7K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a407525c141.tmp'    rename '/private/tmp/RtmperfYBE/file17a407525c141.tmp' (4.9K, reduced: 29.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a407525c141' (34.7K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a407525c141.tmp'    rename '/private/tmp/RtmperfYBE/file17a407525c141.tmp' (4.9K, reduced: 29.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a402da371c9' (4.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a402da371c9.tmp'    rename '/private/tmp/RtmperfYBE/file17a402da371c9.tmp' (3.5K, reduced: 1010B)    # of fragments: 14Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Block 4 of 4Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a402da371c9' (4.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a402da371c9.tmp'    rename '/private/tmp/RtmperfYBE/file17a402da371c9.tmp' (3.5K, reduced: 1010B)    # of fragments: 14Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Block 4 of 4Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a402da371c9' (4.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a402da371c9.tmp'    rename '/private/tmp/RtmperfYBE/file17a402da371c9.tmp' (3.5K, reduced: 1010B)    # of fragments: 14Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a402da371c9' (4.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a402da371c9.tmp'    rename '/private/tmp/RtmperfYBE/file17a402da371c9.tmp' (3.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Block 4 of 4Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a402da371c9' (4.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a402da371c9.tmp'    rename '/private/tmp/RtmperfYBE/file17a402da371c9.tmp' (3.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Block 4 of 4Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a402da371c9' (4.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a402da371c9.tmp'    rename '/private/tmp/RtmperfYBE/file17a402da371c9.tmp' (3.5K, reduced: 1.0K)    # of fragments: 14Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a40465ccc30' (34.7K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a40465ccc30.tmp'    rename '/private/tmp/RtmperfYBE/file17a40465ccc30.tmp' (4.9K, reduced: 29.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 33Block 2 of 33Block 3 of 33Block 4 of 33Block 5 of 33Block 6 of 33Block 7 of 33Block 8 of 33Block 9 of 33Block 10 of 33Block 11 of 33Block 12 of 33Block 13 of 33Block 14 of 33Block 15 of 33Block 16 of 33Block 17 of 33Block 18 of 33Block 19 of 33Block 20 of 33Block 21 of 33Block 22 of 33Block 23 of 33Block 24 of 33Block 25 of 33Block 26 of 33Block 27 of 33Block 28 of 33Block 29 of 33Block 30 of 33Block 31 of 33Block 32 of 33Block 33 of 33Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a40465ccc30' (34.7K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a40465ccc30.tmp'    rename '/private/tmp/RtmperfYBE/file17a40465ccc30.tmp' (4.9K, reduced: 29.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 1Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Block 4 of 4Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading sample file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a40152247e7' (34.7K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a40152247e7.tmp'    rename '/private/tmp/RtmperfYBE/file17a40152247e7.tmp' (4.9K, reduced: 29.8K)    # of fragments: 14Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4049030cf6' (29.3K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4049030cf6.tmp'    rename '/private/tmp/RtmperfYBE/file17a4049030cf6.tmp' (4.2K, reduced: 25.1K)    # of fragments: 14Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 4Block 2 of 4Block 3 of 4Block 4 of 4Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4049030cf6' (29.3K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4049030cf6.tmp'    rename '/private/tmp/RtmperfYBE/file17a4049030cf6.tmp' (4.2K, reduced: 25.1K)    # of fragments: 14Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4049030cf6' (29.3K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4049030cf6.tmp'    rename '/private/tmp/RtmperfYBE/file17a4049030cf6.tmp' (4.2K, reduced: 25.1K)    # of fragments: 14Determining number of SNPs and samples...Reading sample file...Reading genotype file...Block 1 of 33Block 2 of 33Block 3 of 33Block 4 of 33Block 5 of 33Block 6 of 33Block 7 of 33Block 8 of 33Block 9 of 33Block 10 of 33Block 11 of 33Block 12 of 33Block 13 of 33Block 14 of 33Block 15 of 33Block 16 of 33Block 17 of 33Block 18 of 33Block 19 of 33Block 20 of 33Block 21 of 33Block 22 of 33Block 23 of 33Block 24 of 33Block 25 of 33Block 26 of 33Block 27 of 33Block 28 of 33Block 29 of 33Block 30 of 33Block 31 of 33Block 32 of 33Block 33 of 33Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a4049030cf6' (29.3K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a4049030cf6.tmp'    rename '/private/tmp/RtmperfYBE/file17a4049030cf6.tmp' (4.2K, reduced: 25.1K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (87.7K, reduced: 262.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (86.3K, reduced: 264.2K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (87.7K, reduced: 262.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (86.3K, reduced: 264.2K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (87.7K, reduced: 262.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (86.3K, reduced: 264.2K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (91.1K, reduced: 259.3K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (90.6K, reduced: 259.9K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (91.1K, reduced: 259.3K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (90.6K, reduced: 259.9K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (91.1K, reduced: 259.3K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a405400b3c4' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp'    rename '/private/tmp/RtmperfYBE/file17a405400b3c4.tmp' (90.6K, reduced: 259.9K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a406775af3d' (24.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a406775af3d.tmp'    rename '/private/tmp/RtmperfYBE/file17a406775af3d.tmp' (10.9K, reduced: 13.6K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a406775af3d' (24.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a406775af3d.tmp'    rename '/private/tmp/RtmperfYBE/file17a406775af3d.tmp' (10.9K, reduced: 13.6K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a406775af3d' (24.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a406775af3d.tmp'    rename '/private/tmp/RtmperfYBE/file17a406775af3d.tmp' (10.9K, reduced: 13.6K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a406775af3d' (24.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a406775af3d.tmp'    rename '/private/tmp/RtmperfYBE/file17a406775af3d.tmp' (10.2K, reduced: 14.3K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a406775af3d' (24.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a406775af3d.tmp'    rename '/private/tmp/RtmperfYBE/file17a406775af3d.tmp' (10.2K, reduced: 14.3K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a406775af3d' (24.6K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a406775af3d.tmp'    rename '/private/tmp/RtmperfYBE/file17a406775af3d.tmp' (10.2K, reduced: 14.3K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 2Block 2 of 2Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404a27b152' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404a27b152.tmp'    rename '/private/tmp/RtmperfYBE/file17a404a27b152.tmp' (87.7K, reduced: 262.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404a27b152' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404a27b152.tmp'    rename '/private/tmp/RtmperfYBE/file17a404a27b152.tmp' (86.3K, reduced: 264.2K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 500Block 2 of 500Block 3 of 500Block 4 of 500Block 5 of 500Block 6 of 500Block 7 of 500Block 8 of 500Block 9 of 500Block 10 of 500Block 11 of 500Block 12 of 500Block 13 of 500Block 14 of 500Block 15 of 500Block 16 of 500Block 17 of 500Block 18 of 500Block 19 of 500Block 20 of 500Block 21 of 500Block 22 of 500Block 23 of 500Block 24 of 500Block 25 of 500Block 26 of 500Block 27 of 500Block 28 of 500Block 29 of 500Block 30 of 500Block 31 of 500Block 32 of 500Block 33 of 500Block 34 of 500Block 35 of 500Block 36 of 500Block 37 of 500Block 38 of 500Block 39 of 500Block 40 of 500Block 41 of 500Block 42 of 500Block 43 of 500Block 44 of 500Block 45 of 500Block 46 of 500Block 47 of 500Block 48 of 500Block 49 of 500Block 50 of 500Block 51 of 500Block 52 of 500Block 53 of 500Block 54 of 500Block 55 of 500Block 56 of 500Block 57 of 500Block 58 of 500Block 59 of 500Block 60 of 500Block 61 of 500Block 62 of 500Block 63 of 500Block 64 of 500Block 65 of 500Block 66 of 500Block 67 of 500Block 68 of 500Block 69 of 500Block 70 of 500Block 71 of 500Block 72 of 500Block 73 of 500Block 74 of 500Block 75 of 500Block 76 of 500Block 77 of 500Block 78 of 500Block 79 of 500Block 80 of 500Block 81 of 500Block 82 of 500Block 83 of 500Block 84 of 500Block 85 of 500Block 86 of 500Block 87 of 500Block 88 of 500Block 89 of 500Block 90 of 500Block 91 of 500Block 92 of 500Block 93 of 500Block 94 of 500Block 95 of 500Block 96 of 500Block 97 of 500Block 98 of 500Block 99 of 500Block 100 of 500Block 101 of 500Block 102 of 500Block 103 of 500Block 104 of 500Block 105 of 500Block 106 of 500Block 107 of 500Block 108 of 500Block 109 of 500Block 110 of 500Block 111 of 500Block 112 of 500Block 113 of 500Block 114 of 500Block 115 of 500Block 116 of 500Block 117 of 500Block 118 of 500Block 119 of 500Block 120 of 500Block 121 of 500Block 122 of 500Block 123 of 500Block 124 of 500Block 125 of 500Block 126 of 500Block 127 of 500Block 128 of 500Block 129 of 500Block 130 of 500Block 131 of 500Block 132 of 500Block 133 of 500Block 134 of 500Block 135 of 500Block 136 of 500Block 137 of 500Block 138 of 500Block 139 of 500Block 140 of 500Block 141 of 500Block 142 of 500Block 143 of 500Block 144 of 500Block 145 of 500Block 146 of 500Block 147 of 500Block 148 of 500Block 149 of 500Block 150 of 500Block 151 of 500Block 152 of 500Block 153 of 500Block 154 of 500Block 155 of 500Block 156 of 500Block 157 of 500Block 158 of 500Block 159 of 500Block 160 of 500Block 161 of 500Block 162 of 500Block 163 of 500Block 164 of 500Block 165 of 500Block 166 of 500Block 167 of 500Block 168 of 500Block 169 of 500Block 170 of 500Block 171 of 500Block 172 of 500Block 173 of 500Block 174 of 500Block 175 of 500Block 176 of 500Block 177 of 500Block 178 of 500Block 179 of 500Block 180 of 500Block 181 of 500Block 182 of 500Block 183 of 500Block 184 of 500Block 185 of 500Block 186 of 500Block 187 of 500Block 188 of 500Block 189 of 500Block 190 of 500Block 191 of 500Block 192 of 500Block 193 of 500Block 194 of 500Block 195 of 500Block 196 of 500Block 197 of 500Block 198 of 500Block 199 of 500Block 200 of 500Block 201 of 500Block 202 of 500Block 203 of 500Block 204 of 500Block 205 of 500Block 206 of 500Block 207 of 500Block 208 of 500Block 209 of 500Block 210 of 500Block 211 of 500Block 212 of 500Block 213 of 500Block 214 of 500Block 215 of 500Block 216 of 500Block 217 of 500Block 218 of 500Block 219 of 500Block 220 of 500Block 221 of 500Block 222 of 500Block 223 of 500Block 224 of 500Block 225 of 500Block 226 of 500Block 227 of 500Block 228 of 500Block 229 of 500Block 230 of 500Block 231 of 500Block 232 of 500Block 233 of 500Block 234 of 500Block 235 of 500Block 236 of 500Block 237 of 500Block 238 of 500Block 239 of 500Block 240 of 500Block 241 of 500Block 242 of 500Block 243 of 500Block 244 of 500Block 245 of 500Block 246 of 500Block 247 of 500Block 248 of 500Block 249 of 500Block 250 of 500Block 251 of 500Block 252 of 500Block 253 of 500Block 254 of 500Block 255 of 500Block 256 of 500Block 257 of 500Block 258 of 500Block 259 of 500Block 260 of 500Block 261 of 500Block 262 of 500Block 263 of 500Block 264 of 500Block 265 of 500Block 266 of 500Block 267 of 500Block 268 of 500Block 269 of 500Block 270 of 500Block 271 of 500Block 272 of 500Block 273 of 500Block 274 of 500Block 275 of 500Block 276 of 500Block 277 of 500Block 278 of 500Block 279 of 500Block 280 of 500Block 281 of 500Block 282 of 500Block 283 of 500Block 284 of 500Block 285 of 500Block 286 of 500Block 287 of 500Block 288 of 500Block 289 of 500Block 290 of 500Block 291 of 500Block 292 of 500Block 293 of 500Block 294 of 500Block 295 of 500Block 296 of 500Block 297 of 500Block 298 of 500Block 299 of 500Block 300 of 500Block 301 of 500Block 302 of 500Block 303 of 500Block 304 of 500Block 305 of 500Block 306 of 500Block 307 of 500Block 308 of 500Block 309 of 500Block 310 of 500Block 311 of 500Block 312 of 500Block 313 of 500Block 314 of 500Block 315 of 500Block 316 of 500Block 317 of 500Block 318 of 500Block 319 of 500Block 320 of 500Block 321 of 500Block 322 of 500Block 323 of 500Block 324 of 500Block 325 of 500Block 326 of 500Block 327 of 500Block 328 of 500Block 329 of 500Block 330 of 500Block 331 of 500Block 332 of 500Block 333 of 500Block 334 of 500Block 335 of 500Block 336 of 500Block 337 of 500Block 338 of 500Block 339 of 500Block 340 of 500Block 341 of 500Block 342 of 500Block 343 of 500Block 344 of 500Block 345 of 500Block 346 of 500Block 347 of 500Block 348 of 500Block 349 of 500Block 350 of 500Block 351 of 500Block 352 of 500Block 353 of 500Block 354 of 500Block 355 of 500Block 356 of 500Block 357 of 500Block 358 of 500Block 359 of 500Block 360 of 500Block 361 of 500Block 362 of 500Block 363 of 500Block 364 of 500Block 365 of 500Block 366 of 500Block 367 of 500Block 368 of 500Block 369 of 500Block 370 of 500Block 371 of 500Block 372 of 500Block 373 of 500Block 374 of 500Block 375 of 500Block 376 of 500Block 377 of 500Block 378 of 500Block 379 of 500Block 380 of 500Block 381 of 500Block 382 of 500Block 383 of 500Block 384 of 500Block 385 of 500Block 386 of 500Block 387 of 500Block 388 of 500Block 389 of 500Block 390 of 500Block 391 of 500Block 392 of 500Block 393 of 500Block 394 of 500Block 395 of 500Block 396 of 500Block 397 of 500Block 398 of 500Block 399 of 500Block 400 of 500Block 401 of 500Block 402 of 500Block 403 of 500Block 404 of 500Block 405 of 500Block 406 of 500Block 407 of 500Block 408 of 500Block 409 of 500Block 410 of 500Block 411 of 500Block 412 of 500Block 413 of 500Block 414 of 500Block 415 of 500Block 416 of 500Block 417 of 500Block 418 of 500Block 419 of 500Block 420 of 500Block 421 of 500Block 422 of 500Block 423 of 500Block 424 of 500Block 425 of 500Block 426 of 500Block 427 of 500Block 428 of 500Block 429 of 500Block 430 of 500Block 431 of 500Block 432 of 500Block 433 of 500Block 434 of 500Block 435 of 500Block 436 of 500Block 437 of 500Block 438 of 500Block 439 of 500Block 440 of 500Block 441 of 500Block 442 of 500Block 443 of 500Block 444 of 500Block 445 of 500Block 446 of 500Block 447 of 500Block 448 of 500Block 449 of 500Block 450 of 500Block 451 of 500Block 452 of 500Block 453 of 500Block 454 of 500Block 455 of 500Block 456 of 500Block 457 of 500Block 458 of 500Block 459 of 500Block 460 of 500Block 461 of 500Block 462 of 500Block 463 of 500Block 464 of 500Block 465 of 500Block 466 of 500Block 467 of 500Block 468 of 500Block 469 of 500Block 470 of 500Block 471 of 500Block 472 of 500Block 473 of 500Block 474 of 500Block 475 of 500Block 476 of 500Block 477 of 500Block 478 of 500Block 479 of 500Block 480 of 500Block 481 of 500Block 482 of 500Block 483 of 500Block 484 of 500Block 485 of 500Block 486 of 500Block 487 of 500Block 488 of 500Block 489 of 500Block 490 of 500Block 491 of 500Block 492 of 500Block 493 of 500Block 494 of 500Block 495 of 500Block 496 of 500Block 497 of 500Block 498 of 500Block 499 of 500Block 500 of 500Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404a27b152' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404a27b152.tmp'    rename '/private/tmp/RtmperfYBE/file17a404a27b152.tmp' (87.7K, reduced: 262.8K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 500Block 2 of 500Block 3 of 500Block 4 of 500Block 5 of 500Block 6 of 500Block 7 of 500Block 8 of 500Block 9 of 500Block 10 of 500Block 11 of 500Block 12 of 500Block 13 of 500Block 14 of 500Block 15 of 500Block 16 of 500Block 17 of 500Block 18 of 500Block 19 of 500Block 20 of 500Block 21 of 500Block 22 of 500Block 23 of 500Block 24 of 500Block 25 of 500Block 26 of 500Block 27 of 500Block 28 of 500Block 29 of 500Block 30 of 500Block 31 of 500Block 32 of 500Block 33 of 500Block 34 of 500Block 35 of 500Block 36 of 500Block 37 of 500Block 38 of 500Block 39 of 500Block 40 of 500Block 41 of 500Block 42 of 500Block 43 of 500Block 44 of 500Block 45 of 500Block 46 of 500Block 47 of 500Block 48 of 500Block 49 of 500Block 50 of 500Block 51 of 500Block 52 of 500Block 53 of 500Block 54 of 500Block 55 of 500Block 56 of 500Block 57 of 500Block 58 of 500Block 59 of 500Block 60 of 500Block 61 of 500Block 62 of 500Block 63 of 500Block 64 of 500Block 65 of 500Block 66 of 500Block 67 of 500Block 68 of 500Block 69 of 500Block 70 of 500Block 71 of 500Block 72 of 500Block 73 of 500Block 74 of 500Block 75 of 500Block 76 of 500Block 77 of 500Block 78 of 500Block 79 of 500Block 80 of 500Block 81 of 500Block 82 of 500Block 83 of 500Block 84 of 500Block 85 of 500Block 86 of 500Block 87 of 500Block 88 of 500Block 89 of 500Block 90 of 500Block 91 of 500Block 92 of 500Block 93 of 500Block 94 of 500Block 95 of 500Block 96 of 500Block 97 of 500Block 98 of 500Block 99 of 500Block 100 of 500Block 101 of 500Block 102 of 500Block 103 of 500Block 104 of 500Block 105 of 500Block 106 of 500Block 107 of 500Block 108 of 500Block 109 of 500Block 110 of 500Block 111 of 500Block 112 of 500Block 113 of 500Block 114 of 500Block 115 of 500Block 116 of 500Block 117 of 500Block 118 of 500Block 119 of 500Block 120 of 500Block 121 of 500Block 122 of 500Block 123 of 500Block 124 of 500Block 125 of 500Block 126 of 500Block 127 of 500Block 128 of 500Block 129 of 500Block 130 of 500Block 131 of 500Block 132 of 500Block 133 of 500Block 134 of 500Block 135 of 500Block 136 of 500Block 137 of 500Block 138 of 500Block 139 of 500Block 140 of 500Block 141 of 500Block 142 of 500Block 143 of 500Block 144 of 500Block 145 of 500Block 146 of 500Block 147 of 500Block 148 of 500Block 149 of 500Block 150 of 500Block 151 of 500Block 152 of 500Block 153 of 500Block 154 of 500Block 155 of 500Block 156 of 500Block 157 of 500Block 158 of 500Block 159 of 500Block 160 of 500Block 161 of 500Block 162 of 500Block 163 of 500Block 164 of 500Block 165 of 500Block 166 of 500Block 167 of 500Block 168 of 500Block 169 of 500Block 170 of 500Block 171 of 500Block 172 of 500Block 173 of 500Block 174 of 500Block 175 of 500Block 176 of 500Block 177 of 500Block 178 of 500Block 179 of 500Block 180 of 500Block 181 of 500Block 182 of 500Block 183 of 500Block 184 of 500Block 185 of 500Block 186 of 500Block 187 of 500Block 188 of 500Block 189 of 500Block 190 of 500Block 191 of 500Block 192 of 500Block 193 of 500Block 194 of 500Block 195 of 500Block 196 of 500Block 197 of 500Block 198 of 500Block 199 of 500Block 200 of 500Block 201 of 500Block 202 of 500Block 203 of 500Block 204 of 500Block 205 of 500Block 206 of 500Block 207 of 500Block 208 of 500Block 209 of 500Block 210 of 500Block 211 of 500Block 212 of 500Block 213 of 500Block 214 of 500Block 215 of 500Block 216 of 500Block 217 of 500Block 218 of 500Block 219 of 500Block 220 of 500Block 221 of 500Block 222 of 500Block 223 of 500Block 224 of 500Block 225 of 500Block 226 of 500Block 227 of 500Block 228 of 500Block 229 of 500Block 230 of 500Block 231 of 500Block 232 of 500Block 233 of 500Block 234 of 500Block 235 of 500Block 236 of 500Block 237 of 500Block 238 of 500Block 239 of 500Block 240 of 500Block 241 of 500Block 242 of 500Block 243 of 500Block 244 of 500Block 245 of 500Block 246 of 500Block 247 of 500Block 248 of 500Block 249 of 500Block 250 of 500Block 251 of 500Block 252 of 500Block 253 of 500Block 254 of 500Block 255 of 500Block 256 of 500Block 257 of 500Block 258 of 500Block 259 of 500Block 260 of 500Block 261 of 500Block 262 of 500Block 263 of 500Block 264 of 500Block 265 of 500Block 266 of 500Block 267 of 500Block 268 of 500Block 269 of 500Block 270 of 500Block 271 of 500Block 272 of 500Block 273 of 500Block 274 of 500Block 275 of 500Block 276 of 500Block 277 of 500Block 278 of 500Block 279 of 500Block 280 of 500Block 281 of 500Block 282 of 500Block 283 of 500Block 284 of 500Block 285 of 500Block 286 of 500Block 287 of 500Block 288 of 500Block 289 of 500Block 290 of 500Block 291 of 500Block 292 of 500Block 293 of 500Block 294 of 500Block 295 of 500Block 296 of 500Block 297 of 500Block 298 of 500Block 299 of 500Block 300 of 500Block 301 of 500Block 302 of 500Block 303 of 500Block 304 of 500Block 305 of 500Block 306 of 500Block 307 of 500Block 308 of 500Block 309 of 500Block 310 of 500Block 311 of 500Block 312 of 500Block 313 of 500Block 314 of 500Block 315 of 500Block 316 of 500Block 317 of 500Block 318 of 500Block 319 of 500Block 320 of 500Block 321 of 500Block 322 of 500Block 323 of 500Block 324 of 500Block 325 of 500Block 326 of 500Block 327 of 500Block 328 of 500Block 329 of 500Block 330 of 500Block 331 of 500Block 332 of 500Block 333 of 500Block 334 of 500Block 335 of 500Block 336 of 500Block 337 of 500Block 338 of 500Block 339 of 500Block 340 of 500Block 341 of 500Block 342 of 500Block 343 of 500Block 344 of 500Block 345 of 500Block 346 of 500Block 347 of 500Block 348 of 500Block 349 of 500Block 350 of 500Block 351 of 500Block 352 of 500Block 353 of 500Block 354 of 500Block 355 of 500Block 356 of 500Block 357 of 500Block 358 of 500Block 359 of 500Block 360 of 500Block 361 of 500Block 362 of 500Block 363 of 500Block 364 of 500Block 365 of 500Block 366 of 500Block 367 of 500Block 368 of 500Block 369 of 500Block 370 of 500Block 371 of 500Block 372 of 500Block 373 of 500Block 374 of 500Block 375 of 500Block 376 of 500Block 377 of 500Block 378 of 500Block 379 of 500Block 380 of 500Block 381 of 500Block 382 of 500Block 383 of 500Block 384 of 500Block 385 of 500Block 386 of 500Block 387 of 500Block 388 of 500Block 389 of 500Block 390 of 500Block 391 of 500Block 392 of 500Block 393 of 500Block 394 of 500Block 395 of 500Block 396 of 500Block 397 of 500Block 398 of 500Block 399 of 500Block 400 of 500Block 401 of 500Block 402 of 500Block 403 of 500Block 404 of 500Block 405 of 500Block 406 of 500Block 407 of 500Block 408 of 500Block 409 of 500Block 410 of 500Block 411 of 500Block 412 of 500Block 413 of 500Block 414 of 500Block 415 of 500Block 416 of 500Block 417 of 500Block 418 of 500Block 419 of 500Block 420 of 500Block 421 of 500Block 422 of 500Block 423 of 500Block 424 of 500Block 425 of 500Block 426 of 500Block 427 of 500Block 428 of 500Block 429 of 500Block 430 of 500Block 431 of 500Block 432 of 500Block 433 of 500Block 434 of 500Block 435 of 500Block 436 of 500Block 437 of 500Block 438 of 500Block 439 of 500Block 440 of 500Block 441 of 500Block 442 of 500Block 443 of 500Block 444 of 500Block 445 of 500Block 446 of 500Block 447 of 500Block 448 of 500Block 449 of 500Block 450 of 500Block 451 of 500Block 452 of 500Block 453 of 500Block 454 of 500Block 455 of 500Block 456 of 500Block 457 of 500Block 458 of 500Block 459 of 500Block 460 of 500Block 461 of 500Block 462 of 500Block 463 of 500Block 464 of 500Block 465 of 500Block 466 of 500Block 467 of 500Block 468 of 500Block 469 of 500Block 470 of 500Block 471 of 500Block 472 of 500Block 473 of 500Block 474 of 500Block 475 of 500Block 476 of 500Block 477 of 500Block 478 of 500Block 479 of 500Block 480 of 500Block 481 of 500Block 482 of 500Block 483 of 500Block 484 of 500Block 485 of 500Block 486 of 500Block 487 of 500Block 488 of 500Block 489 of 500Block 490 of 500Block 491 of 500Block 492 of 500Block 493 of 500Block 494 of 500Block 495 of 500Block 496 of 500Block 497 of 500Block 498 of 500Block 499 of 500Block 500 of 500Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a404a27b152' (350.5K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a404a27b152.tmp'    rename '/private/tmp/RtmperfYBE/file17a404a27b152.tmp' (86.3K, reduced: 264.2K)    # of fragments: 14Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 3Block 2 of 3Block 3 of 3Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Determining number of SNPs and samples...Including all SNPs.scan.df not given. Assigning scanIDs automatically.Reading SNP files...Reading genotype file...Block 1 of 2Block 2 of 2Writing annotation...Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401af98910' (338.0K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a401af98910.tmp'    rename '/private/tmp/RtmperfYBE/file17a401af98910.tmp' (85.1K, reduced: 252.9K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 1Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401af98910' (338.0K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a401af98910.tmp'    rename '/private/tmp/RtmperfYBE/file17a401af98910.tmp' (84.0K, reduced: 254.0K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 3Block 1 of 3Block 2 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401af98910' (338.0K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a401af98910.tmp'    rename '/private/tmp/RtmperfYBE/file17a401af98910.tmp' (85.1K, reduced: 252.9K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 3Block 1 of 3Block 2 of 3Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401af98910' (338.0K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a401af98910.tmp'    rename '/private/tmp/RtmperfYBE/file17a401af98910.tmp' (84.0K, reduced: 254.0K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 2Block 1 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401af98910' (338.0K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a401af98910.tmp'    rename '/private/tmp/RtmperfYBE/file17a401af98910.tmp' (85.1K, reduced: 252.9K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 2Block 1 of 2Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401af98910' (338.0K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a401af98910.tmp'    rename '/private/tmp/RtmperfYBE/file17a401af98910.tmp' (84.0K, reduced: 254.0K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 500Block 2 of 500Block 3 of 500Block 4 of 500Block 5 of 500Block 6 of 500Block 7 of 500Block 8 of 500Block 9 of 500Block 10 of 500Block 11 of 500Block 12 of 500Block 13 of 500Block 14 of 500Block 15 of 500Block 16 of 500Block 17 of 500Block 18 of 500Block 19 of 500Block 20 of 500Block 21 of 500Block 22 of 500Block 23 of 500Block 24 of 500Block 25 of 500Block 26 of 500Block 27 of 500Block 28 of 500Block 29 of 500Block 30 of 500Block 31 of 500Block 32 of 500Block 33 of 500Block 34 of 500Block 35 of 500Block 36 of 500Block 37 of 500Block 38 of 500Block 39 of 500Block 40 of 500Block 41 of 500Block 42 of 500Block 43 of 500Block 44 of 500Block 45 of 500Block 46 of 500Block 47 of 500Block 48 of 500Block 49 of 500Block 50 of 500Block 51 of 500Block 52 of 500Block 53 of 500Block 54 of 500Block 55 of 500Block 56 of 500Block 57 of 500Block 58 of 500Block 58 of 500Block 59 of 500Block 60 of 500Block 61 of 500Block 62 of 500Block 63 of 500Block 64 of 500Block 65 of 500Block 66 of 500Block 67 of 500Block 68 of 500Block 69 of 500Block 70 of 500Block 71 of 500Block 72 of 500Block 73 of 500Block 74 of 500Block 75 of 500Block 76 of 500Block 77 of 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of 500Block 142 of 500Block 143 of 500Block 144 of 500Block 145 of 500Block 146 of 500Block 147 of 500Block 148 of 500Block 149 of 500Block 150 of 500Block 151 of 500Block 152 of 500Block 153 of 500Block 154 of 500Block 155 of 500Block 156 of 500Block 157 of 500Block 158 of 500Block 159 of 500Block 160 of 500Block 161 of 500Block 162 of 500Block 163 of 500Block 164 of 500Block 165 of 500Block 166 of 500Block 167 of 500Block 168 of 500Block 169 of 500Block 170 of 500Block 171 of 500Block 172 of 500Block 173 of 500Block 174 of 500Block 175 of 500Block 176 of 500Block 177 of 500Block 178 of 500Block 179 of 500Block 180 of 500Block 181 of 500Block 182 of 500Block 183 of 500Block 184 of 500Block 185 of 500Block 186 of 500Block 187 of 500Block 188 of 500Block 189 of 500Block 190 of 500Block 191 of 500Block 192 of 500Block 193 of 500Block 194 of 500Block 195 of 500Block 196 of 500Block 197 of 500Block 198 of 500Block 199 of 500Block 200 of 500Block 201 of 500Block 202 of 500Block 203 of 500Block 204 of 500Block 205 of 500Block 206 of 500Block 207 of 500Block 208 of 500Block 209 of 500Block 210 of 500Block 211 of 500Block 212 of 500Block 213 of 500Block 214 of 500Block 215 of 500Block 216 of 500Block 217 of 500Block 218 of 500Block 219 of 500Block 220 of 500Block 221 of 500Block 222 of 500Block 223 of 500Block 224 of 500Block 225 of 500Block 226 of 500Block 227 of 500Block 228 of 500Block 229 of 500Block 230 of 500Block 231 of 500Block 232 of 500Block 233 of 500Block 234 of 500Block 235 of 500Block 236 of 500Block 237 of 500Block 238 of 500Block 239 of 500Block 240 of 500Block 241 of 500Block 242 of 500Block 243 of 500Block 244 of 500Block 245 of 500Block 246 of 500Block 247 of 500Block 247 of 500Block 248 of 500Block 249 of 500Block 250 of 500Block 251 of 500Block 252 of 500Block 253 of 500Block 254 of 500Block 255 of 500Block 256 of 500Block 257 of 500Block 258 of 500Block 259 of 500Block 260 of 500Block 261 of 500Block 262 of 500Block 263 of 500Block 264 of 500Block 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500Block 326 of 500Block 327 of 500Block 328 of 500Block 329 of 500Block 330 of 500Block 331 of 500Block 332 of 500Block 333 of 500Block 334 of 500Block 335 of 500Block 336 of 500Block 337 of 500Block 338 of 500Block 339 of 500Block 340 of 500Block 341 of 500Block 342 of 500Block 343 of 500Block 344 of 500Block 345 of 500Block 346 of 500Block 347 of 500Block 348 of 500Block 349 of 500Block 350 of 500Block 351 of 500Block 352 of 500Block 353 of 500Block 354 of 500Block 355 of 500Block 356 of 500Block 357 of 500Block 358 of 500Block 359 of 500Block 360 of 500Block 361 of 500Block 362 of 500Block 363 of 500Block 364 of 500Block 365 of 500Block 366 of 500Block 367 of 500Block 368 of 500Block 369 of 500Block 370 of 500Block 371 of 500Block 372 of 500Block 373 of 500Block 374 of 500Block 375 of 500Block 376 of 500Block 377 of 500Block 378 of 500Block 379 of 500Block 380 of 500Block 380 of 500Block 381 of 500Block 382 of 500Block 383 of 500Block 384 of 500Block 385 of 500Block 386 of 500Block 387 of 500Block 388 of 500Block 389 of 500Block 390 of 500Block 391 of 500Block 392 of 500Block 393 of 500Block 394 of 500Block 395 of 500Block 396 of 500Block 397 of 500Block 398 of 500Block 399 of 500Block 400 of 500Block 401 of 500Block 402 of 500Block 403 of 500Block 404 of 500Block 405 of 500Block 406 of 500Block 407 of 500Block 408 of 500Block 409 of 500Block 410 of 500Block 411 of 500Block 412 of 500Block 413 of 500Block 414 of 500Block 415 of 500Block 416 of 500Block 417 of 500Block 418 of 500Block 419 of 500Block 420 of 500Block 421 of 500Block 422 of 500Block 423 of 500Block 424 of 500Block 425 of 500Block 426 of 500Block 427 of 500Block 428 of 500Block 429 of 500Block 430 of 500Block 431 of 500Block 432 of 500Block 433 of 500Block 434 of 500Block 435 of 500Block 436 of 500Block 437 of 500Block 438 of 500Block 439 of 500Block 440 of 500Block 441 of 500Block 442 of 500Block 443 of 500Block 444 of 500Block 445 of 500Block 446 of 500Block 447 of 500Block 448 of 500Block 449 of 500Block 450 of 500Block 451 of 500Block 452 of 500Block 453 of 500Block 454 of 500Block 455 of 500Block 456 of 500Block 457 of 500Block 458 of 500Block 459 of 500Block 460 of 500Block 461 of 500Block 462 of 500Block 463 of 500Block 464 of 500Block 465 of 500Block 466 of 500Block 467 of 500Block 468 of 500Block 469 of 500Block 470 of 500Block 471 of 500Block 472 of 500Block 473 of 500Block 474 of 500Block 475 of 500Block 476 of 500Block 477 of 500Block 478 of 500Block 479 of 500Block 480 of 500Block 481 of 500Block 482 of 500Block 483 of 500Block 484 of 500Block 485 of 500Block 486 of 500Block 487 of 500Block 488 of 500Block 489 of 500Block 490 of 500Block 491 of 500Block 492 of 500Block 493 of 500Block 494 of 500Block 495 of 500Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401af98910' (338.0K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a401af98910.tmp'    rename '/private/tmp/RtmperfYBE/file17a401af98910.tmp' (85.1K, reduced: 252.9K)    # of fragments: 14Determining number of SNPs and samples...Reading SNP files...Reading genotype file...Block 1 of 500Block 2 of 500Block 3 of 500Block 4 of 500Block 5 of 500Block 6 of 500Block 7 of 500Block 8 of 500Block 9 of 500Block 10 of 500Block 11 of 500Block 12 of 500Block 13 of 500Block 14 of 500Block 15 of 500Block 16 of 500Block 17 of 500Block 18 of 500Block 19 of 500Block 20 of 500Block 21 of 500Block 22 of 500Block 23 of 500Block 24 of 500Block 25 of 500Block 26 of 500Block 27 of 500Block 28 of 500Block 29 of 500Block 30 of 500Block 31 of 500Block 32 of 500Block 33 of 500Block 34 of 500Block 35 of 500Block 36 of 500Block 37 of 500Block 38 of 500Block 39 of 500Block 40 of 500Block 41 of 500Block 42 of 500Block 43 of 500Block 44 of 500Block 45 of 500Block 46 of 500Block 47 of 500Block 48 of 500Block 49 of 500Block 50 of 500Block 51 of 500Block 52 of 500Block 53 of 500Block 54 of 500Block 55 of 500Block 56 of 500Block 57 of 500Block 58 of 500Block 58 of 500Block 59 of 500Block 60 of 500Block 61 of 500Block 62 of 500Block 63 of 500Block 64 of 500Block 65 of 500Block 66 of 500Block 67 of 500Block 68 of 500Block 69 of 500Block 70 of 500Block 71 of 500Block 72 of 500Block 73 of 500Block 74 of 500Block 75 of 500Block 76 of 500Block 77 of 500Block 78 of 500Block 79 of 500Block 80 of 500Block 81 of 500Block 82 of 500Block 83 of 500Block 84 of 500Block 85 of 500Block 86 of 500Block 87 of 500Block 88 of 500Block 89 of 500Block 90 of 500Block 91 of 500Block 92 of 500Block 93 of 500Block 94 of 500Block 95 of 500Block 96 of 500Block 97 of 500Block 98 of 500Block 99 of 500Block 100 of 500Block 101 of 500Block 102 of 500Block 103 of 500Block 104 of 500Block 105 of 500Block 106 of 500Block 107 of 500Block 108 of 500Block 109 of 500Block 110 of 500Block 111 of 500Block 112 of 500Block 113 of 500Block 114 of 500Block 115 of 500Block 116 of 500Block 117 of 500Block 118 of 500Block 119 of 500Block 120 of 500Block 121 of 500Block 122 of 500Block 123 of 500Block 124 of 500Block 125 of 500Block 126 of 500Block 127 of 500Block 128 of 500Block 129 of 500Block 130 of 500Block 131 of 500Block 132 of 500Block 133 of 500Block 134 of 500Block 135 of 500Block 136 of 500Block 137 of 500Block 138 of 500Block 139 of 500Block 140 of 500Block 141 of 500Block 142 of 500Block 143 of 500Block 144 of 500Block 145 of 500Block 146 of 500Block 147 of 500Block 148 of 500Block 149 of 500Block 150 of 500Block 151 of 500Block 152 of 500Block 153 of 500Block 154 of 500Block 155 of 500Block 156 of 500Block 157 of 500Block 158 of 500Block 159 of 500Block 160 of 500Block 161 of 500Block 162 of 500Block 163 of 500Block 164 of 500Block 165 of 500Block 166 of 500Block 167 of 500Block 168 of 500Block 169 of 500Block 170 of 500Block 171 of 500Block 172 of 500Block 173 of 500Block 174 of 500Block 175 of 500Block 176 of 500Block 177 of 500Block 178 of 500Block 179 of 500Block 180 of 500Block 181 of 500Block 182 of 500Block 183 of 500Block 184 of 500Block 185 of 500Block 186 of 500Block 187 of 500Block 188 of 500Block 189 of 500Block 190 of 500Block 191 of 500Block 192 of 500Block 193 of 500Block 194 of 500Block 195 of 500Block 196 of 500Block 197 of 500Block 198 of 500Block 199 of 500Block 200 of 500Block 201 of 500Block 202 of 500Block 203 of 500Block 204 of 500Block 205 of 500Block 206 of 500Block 207 of 500Block 208 of 500Block 209 of 500Block 210 of 500Block 211 of 500Block 212 of 500Block 213 of 500Block 214 of 500Block 215 of 500Block 216 of 500Block 217 of 500Block 218 of 500Block 219 of 500Block 220 of 500Block 221 of 500Block 222 of 500Block 223 of 500Block 224 of 500Block 225 of 500Block 226 of 500Block 227 of 500Block 228 of 500Block 229 of 500Block 230 of 500Block 231 of 500Block 232 of 500Block 233 of 500Block 234 of 500Block 235 of 500Block 236 of 500Block 237 of 500Block 238 of 500Block 239 of 500Block 240 of 500Block 241 of 500Block 242 of 500Block 243 of 500Block 244 of 500Block 245 of 500Block 246 of 500Block 247 of 500Block 247 of 500Block 248 of 500Block 249 of 500Block 250 of 500Block 251 of 500Block 252 of 500Block 253 of 500Block 254 of 500Block 255 of 500Block 256 of 500Block 257 of 500Block 258 of 500Block 259 of 500Block 260 of 500Block 261 of 500Block 262 of 500Block 263 of 500Block 264 of 500Block 265 of 500Block 266 of 500Block 267 of 500Block 268 of 500Block 268 of 500Block 269 of 500Block 270 of 500Block 271 of 500Block 272 of 500Block 273 of 500Block 274 of 500Block 275 of 500Block 276 of 500Block 277 of 500Block 278 of 500Block 279 of 500Block 280 of 500Block 281 of 500Block 282 of 500Block 283 of 500Block 284 of 500Block 285 of 500Block 286 of 500Block 287 of 500Block 288 of 500Block 289 of 500Block 290 of 500Block 291 of 500Block 292 of 500Block 293 of 500Block 294 of 500Block 295 of 500Block 296 of 500Block 297 of 500Block 298 of 500Block 298 of 500Block 299 of 500Block 300 of 500Block 301 of 500Block 302 of 500Block 303 of 500Block 304 of 500Block 305 of 500Block 306 of 500Block 307 of 500Block 308 of 500Block 309 of 500Block 310 of 500Block 311 of 500Block 312 of 500Block 313 of 500Block 314 of 500Block 315 of 500Block 316 of 500Block 317 of 500Block 318 of 500Block 319 of 500Block 320 of 500Block 321 of 500Block 322 of 500Block 323 of 500Block 324 of 500Block 325 of 500Block 326 of 500Block 327 of 500Block 328 of 500Block 329 of 500Block 330 of 500Block 331 of 500Block 332 of 500Block 333 of 500Block 334 of 500Block 335 of 500Block 336 of 500Block 337 of 500Block 338 of 500Block 339 of 500Block 340 of 500Block 341 of 500Block 342 of 500Block 343 of 500Block 344 of 500Block 345 of 500Block 346 of 500Block 347 of 500Block 348 of 500Block 349 of 500Block 350 of 500Block 351 of 500Block 352 of 500Block 353 of 500Block 354 of 500Block 355 of 500Block 356 of 500Block 357 of 500Block 358 of 500Block 359 of 500Block 360 of 500Block 361 of 500Block 362 of 500Block 363 of 500Block 364 of 500Block 365 of 500Block 366 of 500Block 367 of 500Block 368 of 500Block 369 of 500Block 370 of 500Block 371 of 500Block 372 of 500Block 373 of 500Block 374 of 500Block 375 of 500Block 376 of 500Block 377 of 500Block 378 of 500Block 379 of 500Block 380 of 500Block 380 of 500Block 381 of 500Block 382 of 500Block 383 of 500Block 384 of 500Block 385 of 500Block 386 of 500Block 387 of 500Block 388 of 500Block 389 of 500Block 390 of 500Block 391 of 500Block 392 of 500Block 393 of 500Block 394 of 500Block 395 of 500Block 396 of 500Block 397 of 500Block 398 of 500Block 399 of 500Block 400 of 500Block 401 of 500Block 402 of 500Block 403 of 500Block 404 of 500Block 405 of 500Block 406 of 500Block 407 of 500Block 408 of 500Block 409 of 500Block 410 of 500Block 411 of 500Block 412 of 500Block 413 of 500Block 414 of 500Block 415 of 500Block 416 of 500Block 417 of 500Block 418 of 500Block 419 of 500Block 420 of 500Block 421 of 500Block 422 of 500Block 423 of 500Block 424 of 500Block 425 of 500Block 426 of 500Block 427 of 500Block 428 of 500Block 429 of 500Block 430 of 500Block 431 of 500Block 432 of 500Block 433 of 500Block 434 of 500Block 435 of 500Block 436 of 500Block 437 of 500Block 438 of 500Block 439 of 500Block 440 of 500Block 441 of 500Block 442 of 500Block 443 of 500Block 444 of 500Block 445 of 500Block 446 of 500Block 447 of 500Block 448 of 500Block 449 of 500Block 450 of 500Block 451 of 500Block 452 of 500Block 453 of 500Block 454 of 500Block 455 of 500Block 456 of 500Block 457 of 500Block 458 of 500Block 459 of 500Block 460 of 500Block 461 of 500Block 462 of 500Block 463 of 500Block 464 of 500Block 465 of 500Block 466 of 500Block 467 of 500Block 468 of 500Block 469 of 500Block 470 of 500Block 471 of 500Block 472 of 500Block 473 of 500Block 474 of 500Block 475 of 500Block 476 of 500Block 477 of 500Block 478 of 500Block 479 of 500Block 480 of 500Block 481 of 500Block 482 of 500Block 483 of 500Block 484 of 500Block 485 of 500Block 486 of 500Block 487 of 500Block 488 of 500Block 489 of 500Block 490 of 500Block 491 of 500Block 492 of 500Block 493 of 500Block 494 of 500Block 495 of 500Writing annotation...Compressing...Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a401af98910' (338.0K)    # of fragments: 30    save to '/private/tmp/RtmperfYBE/file17a401af98910.tmp'    rename '/private/tmp/RtmperfYBE/file17a401af98910.tmp' (84.0K, reduced: 254.0K)    # of fragments: 14All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.All row numbers refer to row in the full pedigree (not just within family).  Correct current problems and rerun pedigreeCheck.There may be additional problems not investigated because of the current problems.Checking SNPs against map fileChecking sample data and genotypes in each line of ped fileChecking SNPs against map fileChecking sample data and genotypes in each line of ped fileChecking SNPs against map fileChecking sample data and genotypes in each line of ped fileChecking SNPs against map fileChecking sample data and genotypes in each line of ped filewriting block 1 of 1: scans 1-20x being coerced from class: matrix to data.tableChecking SNPs against map fileChecking sample data and genotypes in each line of ped fileChecking SNPs against map fileChecking sample data and genotypes in each line of ped filewriting block 1 of 1: scans 1-20x being coerced from class: matrix to data.tableChecking SNPs against map fileChecking sample data and genotypes in each line of ped filewriting block 1 of 1: scans 1-3x being coerced from class: matrix to data.tablewriting block 1 of 1: scans 1-3x being coerced from class: matrix to data.tableblock number= 1 vector index= 1block number= 1 vector index= 1block number= 1 vector index= 1block number= 2 vector index= 51block number= 3 vector index= 101block number= 4 vector index= 151block number= 5 vector index= 201block number= 6 vector index= 251block number= 1 vector index= 1block number= 2 vector index= 2block number= 3 vector index= 3block number= 4 vector index= 4block number= 5 vector index= 5block number= 6 vector index= 6block number= 7 vector index= 7block number= 8 vector index= 8block number= 9 vector index= 9block number= 10 vector index= 10block number= 11 vector index= 11block number= 12 vector index= 12block number= 13 vector index= 13block number= 14 vector index= 14block number= 15 vector index= 15block number= 16 vector index= 16block number= 17 vector index= 17block number= 18 vector index= 18block number= 19 vector index= 19block number= 20 vector index= 20block number= 21 vector index= 21block number= 22 vector index= 22block number= 23 vector index= 23block number= 24 vector index= 24block number= 25 vector index= 25block number= 26 vector index= 26block number= 27 vector index= 27block number= 28 vector index= 28block number= 29 vector index= 29block number= 30 vector index= 30block number= 31 vector index= 31block number= 32 vector index= 32block number= 33 vector index= 33block number= 34 vector index= 34block number= 35 vector index= 35block number= 36 vector index= 36block number= 37 vector index= 37block number= 38 vector index= 38block number= 39 vector index= 39block number= 40 vector index= 40block number= 41 vector index= 41block number= 42 vector index= 42block number= 43 vector index= 43block number= 44 vector index= 44block number= 45 vector index= 45block number= 46 vector index= 46block number= 47 vector index= 47block number= 48 vector index= 48block number= 49 vector index= 49block number= 50 vector index= 50block number= 51 vector index= 51block number= 52 vector index= 52block number= 53 vector index= 53block number= 54 vector index= 54block number= 55 vector index= 55block number= 56 vector index= 56block number= 57 vector index= 57block number= 58 vector index= 58block number= 59 vector index= 59block number= 60 vector index= 60block number= 61 vector index= 61block number= 62 vector index= 62block number= 63 vector index= 63block number= 64 vector index= 64block number= 65 vector index= 65block number= 66 vector index= 66block number= 67 vector index= 67block number= 68 vector index= 68block number= 69 vector index= 69block number= 70 vector index= 70block number= 71 vector index= 71block number= 72 vector index= 72block number= 73 vector index= 73block number= 74 vector index= 74block number= 75 vector index= 75block number= 76 vector index= 76block number= 77 vector index= 77block number= 78 vector index= 78block number= 79 vector index= 79block number= 80 vector index= 80block number= 81 vector index= 81block number= 82 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vector index= 254block number= 255 vector index= 255block number= 256 vector index= 256block number= 257 vector index= 257block number= 258 vector index= 258block number= 259 vector index= 259block number= 260 vector index= 260sample 10 of 20sample 20 of 20Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a40268b6b42' (3.4K)    # of fragments: 22    save to '/private/tmp/RtmperfYBE/file17a40268b6b42.tmp'    rename '/private/tmp/RtmperfYBE/file17a40268b6b42.tmp' (3.2K, reduced: 132B)    # of fragments: 11working on genotypegenotype - looping over samplesAll variables match.sample 10 of 10Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a40b2ecdd3' (2.6K)    # of fragments: 22    save to '/private/tmp/RtmperfYBE/file17a40b2ecdd3.tmp'    rename '/private/tmp/RtmperfYBE/file17a40b2ecdd3.tmp' (2.5K, reduced: 132B)    # of fragments: 11working on genotypegenotype - looping over samplesAll variables match.sample 10 of 20sample 20 of 20Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a402dcadd61' (3.4K)    # of fragments: 22    save to '/private/tmp/RtmperfYBE/file17a402dcadd61.tmp'    rename '/private/tmp/RtmperfYBE/file17a402dcadd61.tmp' (3.2K, reduced: 132B)    # of fragments: 11sample 10 of 10Clean up the fragments of GDS file:    open the file '/private/tmp/RtmperfYBE/file17a40618c22c3' (2.6K)    # of fragments: 22    save to '/private/tmp/RtmperfYBE/file17a40618c22c3.tmp'    rename '/private/tmp/RtmperfYBE/file17a40618c22c3.tmp' (2.5K, reduced: 132B)    # of fragments: 11Loading required namespace: snpStatsStart file conversion from VCF to SNP GDS ...Method: extracting biallelic SNPsNumber of samples: 5Parsing "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/VariantAnnotation/extdata/chr22.vcf.gz" ...import 9969 variants.+ genotype   { Bit2 5x9969, 12.2K } *Optimize the access efficiency ...Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4060a3af20' (73.0K)    # of fragments: 46    save to '/tmp/RtmperfYBE/file17a4060a3af20.tmp'    rename '/tmp/RtmperfYBE/file17a4060a3af20.tmp' (72.7K, reduced: 312B)    # of fragments: 20Block 1 of 10... 1000 SNPsx being coerced from class: matrix to data.tableBlock 2 of 10... 1000 SNPsx being coerced from class: matrix to data.tableBlock 3 of 10... 1000 SNPsx being coerced from class: matrix to data.tableBlock 4 of 10... 1000 SNPsx being coerced from class: matrix to data.tableBlock 5 of 10... 1000 SNPsx being coerced from class: matrix to data.tableBlock 6 of 10... 1000 SNPsx being coerced from class: matrix to data.tableBlock 7 of 10... 1000 SNPsx being coerced from class: matrix to data.tableBlock 8 of 10... 1000 SNPsx being coerced from class: matrix to data.tableBlock 9 of 10... 1000 SNPsx being coerced from class: matrix to data.tableBlock 10 of 10... 969 SNPsx being coerced from class: matrix to data.tableBlock 1 of 1... 3 SNPsx being coerced from class: matrix to data.tableBlock 1 of 1... 3 SNPsx being coerced from class: matrix to data.tableBlock 1 of 1... 3 SNPsx being coerced from class: matrix to data.tableBlock 1 of 1... 3 SNPsx being coerced from class: matrix to data.tableBlock 1 of 1... 3 SNPsx being coerced from class: matrix to data.tableBlock 1 of 1... 3 SNPsx being coerced from class: matrix to data.tableBlock 1 of 1... 3 SNPsx being coerced from class: matrix to data.tableBlock 1 of 1... 3 SNPsx being coerced from class: matrix to data.tableBlock 1 of 3... 2 SNPsx being coerced from class: matrix to data.tableBlock 2 of 3... 4 SNPsx being coerced from class: matrix to data.tableBlock 3 of 3... 2 SNPsx being coerced from class: matrix to data.tableBlock 1 of 3... 0 SNPsBlock 2 of 3... 1 SNPsx being coerced from class: matrix to data.tableBlock 3 of 3... 2 SNPsx being coerced from class: matrix to data.tableStart file conversion from VCF to SNP GDS ...Method: extracting biallelic SNPsNumber of samples: 3Parsing "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 '/tmp/RtmperfYBE/file17a4015034977' (2.9K)    # of fragments: 46    save to '/tmp/RtmperfYBE/file17a4015034977.tmp'    rename '/tmp/RtmperfYBE/file17a4015034977.tmp' (2.6K, reduced: 312B)    # of fragments: 20Block 1 of 1... 2 SNPsx being coerced from class: matrix to data.tableStart file conversion from VCF to SNP GDS ...Method: extracting biallelic SNPsNumber of samples: 3Parsing "/tmp/RtmperfYBE/file17a40acc2e68" ...import 2 variants.+ genotype   { Bit2 3x2, 2B } *Optimize the access efficiency ...Clean up the fragments of GDS file:    open the file '/tmp/RtmperfYBE/file17a4062fab361' (2.9K)    # of fragments: 46    save to '/tmp/RtmperfYBE/file17a4062fab361.tmp'    rename '/tmp/RtmperfYBE/file17a4062fab361.tmp' (2.6K, reduced: 312B)    # of fragments: 20Block 1 of 1... 5 SNPsx being coerced from class: matrix to data.tableChecked 5 SNPsBlock 1 of 1... 5 SNPsx being coerced from class: matrix to data.tableBlock 1 of 1... 5 SNPsx being coerced from class: matrix to data.tableBlock 1 of 1... 5 SNPsx being coerced from class: matrix to data.tableChecked 5 SNPsBlock 1 of 1... 3 SNPsx being coerced from class: matrix to data.tableExcluding 1 genoData samples from checkExcluding 2 genoData SNPs from checkNote, sample order in VCF differs from genoDataChecked 3 SNPsRUNIT TEST PROTOCOL -- Fri Dec 12 05:44:41 2025 *********************************************** Number of test functions: 211 Number of errors: 0 Number of failures: 0  1 Test Suite : GWASTools RUnit Tests - 211 test functions, 0 errors, 0 failuresNumber of test functions: 211 Number of errors: 0 Number of failures: 0 There were 50 or more warnings (use warnings() to see the first 50)> > proc.time()   user  system elapsed 189.192  26.460 226.608