Xiuwen Zheng
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/SNPRelate |
| git_branch: RELEASE_3_14 |
| git_last_commit: 8fcd837 |
| git_last_commit_date: 2021-10-26 12:15:42 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:23 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the SNPRelate package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SNPRelate.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1831/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SNPRelate 1.28.0 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SNPRelate |
| Version: 1.28.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SNPRelate.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SNPRelate_1.28.0.tar.gz |
| StartedAt: 2022-04-13 03:14:04 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 03:17:53 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 228.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SNPRelate.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SNPRelate.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SNPRelate_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SNPRelate.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'SNPRelate/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SNPRelate' version '1.28.0' * 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 whether package 'SNPRelate' 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... OK * 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/libs/i386/SNPRelate.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/libs/x64/SNPRelate.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SNPRelate.Rcheck/00check.log' for details.
SNPRelate.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SNPRelate_1.28.0.tar.gz && rm -rf SNPRelate.buildbin-libdir && mkdir SNPRelate.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SNPRelate.buildbin-libdir SNPRelate_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SNPRelate_1.28.0.zip && rm SNPRelate_1.28.0.tar.gz SNPRelate_1.28.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
66 1208k 66 797k 0 0 924k 0 0:00:01 --:--:-- 0:00:01 925k
100 1208k 100 1208k 0 0 1075k 0 0:00:01 0:00:01 --:--:-- 1075k
install for i386
* installing *source* package 'SNPRelate' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvToGDS.cpp -o ConvToGDS.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_SNPRelate.c -o R_SNPRelate.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SNPRelate.cpp -o SNPRelate.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ThreadPool.cpp -o ThreadPool.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dGenGWAS.cpp -o dGenGWAS.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dVect.cpp -o dVect.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genBeta.cpp -o genBeta.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genEIGMIX.cpp -o genEIGMIX.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genFst.cpp -o genFst.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genHWE.cpp -o genHWE.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genIBD.cpp -o genIBD.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genIBS.cpp -o genIBS.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genKING.cpp -o genKING.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genLD.cpp -o genLD.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genPCA.cpp -o genPCA.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genSlideWin.cpp -o genSlideWin.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SNPRelate.dll tmp.def ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/SNPRelate.buildbin-libdir/00LOCK-SNPRelate/00new/SNPRelate/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SNPRelate'
finding HTML links ... done
SNPGDSFileClass-class html
SNPRelate-package html
hapmap_geno html
snpgdsAdmixPlot html
snpgdsAdmixProp html
snpgdsAlleleSwitch html
snpgdsApartSelection html
snpgdsBED2GDS html
finding level-2 HTML links ... done
snpgdsClose html
snpgdsCombineGeno html
snpgdsCreateGeno html
snpgdsCreateGenoSet html
snpgdsCutTree html
snpgdsDiss html
snpgdsDrawTree html
snpgdsEIGMIX html
snpgdsErrMsg html
snpgdsExampleFileName html
snpgdsFst html
snpgdsGDS2BED html
snpgdsGDS2Eigen html
snpgdsGDS2PED html
snpgdsGEN2GDS html
snpgdsGRM html
snpgdsGetGeno html
snpgdsHCluster html
snpgdsHWE html
snpgdsIBDKING html
snpgdsIBDMLE html
snpgdsIBDMLELogLik html
snpgdsIBDMoM html
snpgdsIBDSelection html
snpgdsIBS html
snpgdsIBSNum html
snpgdsIndInb html
snpgdsIndInbCoef html
snpgdsIndivBeta html
snpgdsLDMat html
snpgdsLDpair html
snpgdsLDpruning html
snpgdsMergeGRM html
snpgdsOpen html
snpgdsOption html
snpgdsPCA html
snpgdsPCACorr html
snpgdsPCASNPLoading html
snpgdsPCASampLoading html
snpgdsPED2GDS html
snpgdsPairIBD html
snpgdsPairIBDMLELogLik html
snpgdsPairScore html
snpgdsSNPList html
snpgdsSNPListClass html
snpgdsSNPListIntersect html
snpgdsSNPRateFreq html
snpgdsSampMissRate html
snpgdsSelectSNP html
snpgdsSlidingWindow html
snpgdsSummary html
snpgdsTranspose html
snpgdsVCF2GDS html
snpgdsVCF2GDS_R html
** 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
install for x64
* installing *source* package 'SNPRelate' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ConvToGDS.cpp -o ConvToGDS.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_SNPRelate.c -o R_SNPRelate.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SNPRelate.cpp -o SNPRelate.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ThreadPool.cpp -o ThreadPool.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dGenGWAS.cpp -o dGenGWAS.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dVect.cpp -o dVect.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genBeta.cpp -o genBeta.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genEIGMIX.cpp -o genEIGMIX.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genFst.cpp -o genFst.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genHWE.cpp -o genHWE.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genIBD.cpp -o genIBD.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genIBS.cpp -o genIBS.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genKING.cpp -o genKING.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genLD.cpp -o genLD.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genPCA.cpp -o genPCA.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I. -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genSlideWin.cpp -o genSlideWin.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SNPRelate.dll tmp.def ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/SNPRelate.buildbin-libdir/SNPRelate/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SNPRelate' as SNPRelate_1.28.0.zip
* DONE (SNPRelate)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SNPRelate' successfully unpacked and MD5 sums checked
|
SNPRelate.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("SNPRelate")
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Genetic Relationship Matrix (GRM, GCTA):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 1,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:13 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:13 2022 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 2,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:13 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:14 2022 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:14 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:16:15 2022 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:15 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:15 2022 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 1,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:15 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:16 2022 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 2,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:16 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:16 2022 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:16 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:17 2022 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Writing ...
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:17 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:17 2022 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 1,000
using 1 thread
method: covariance
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 1,000
using 1 thread
method: correlation
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
FUNCTION: SNPGDSFileClass
FUNCTION: SNPRelate-package
Start file conversion from PLINK BED to SNP GDS ...
BED file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz"
SNP-major mode (Sample X SNP), 45.7K
FAM file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz"
BIM file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz"
Wed Apr 13 03:16:21 2022 (store sample id, snp id, position, and chromosome)
start writing: 60 samples, 5000 SNPs ...
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:21 2022 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
Principal Component Analysis (PCA) on genotypes:
Excluding 203 SNPs on non-autosomes
Excluding 28 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 60
# of SNPs: 4,769
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 124273
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:21 2022 (internal increment: 53996)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:21 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:16:21 2022 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:16:21 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:16:22 2022 Done.
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:16:23 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:23 2022 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 200
using 1 thread
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 55417
FUNCTION: hapmap_geno
FUNCTION: snpgdsAdmixPlot
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:24 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:24 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:16:24 2022 Done.
FUNCTION: snpgdsAdmixProp
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:24 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:24 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:16:24 2022 Done.
FUNCTION: snpgdsAlleleSwitch
Strand-switching at 50 SNP locus/loci.
Unable to determine switching at 10 SNP locus/loci.
FUNCTION: snpgdsApartSelection
Wed Apr 13 03:16:25 2022 Chromosome 1, # of SNPs: 367
Wed Apr 13 03:16:25 2022 Chromosome 2, # of SNPs: 367
Wed Apr 13 03:16:25 2022 Chromosome 3, # of SNPs: 317
Wed Apr 13 03:16:25 2022 Chromosome 4, # of SNPs: 295
Wed Apr 13 03:16:25 2022 Chromosome 5, # of SNPs: 295
Wed Apr 13 03:16:25 2022 Chromosome 6, # of SNPs: 283
Wed Apr 13 03:16:25 2022 Chromosome 7, # of SNPs: 245
Wed Apr 13 03:16:25 2022 Chromosome 8, # of SNPs: 234
Wed Apr 13 03:16:25 2022 Chromosome 9, # of SNPs: 202
Wed Apr 13 03:16:25 2022 Chromosome 10, # of SNPs: 224
Wed Apr 13 03:16:25 2022 Chromosome 11, # of SNPs: 223
Wed Apr 13 03:16:25 2022 Chromosome 12, # of SNPs: 208
Wed Apr 13 03:16:25 2022 Chromosome 13, # of SNPs: 172
Wed Apr 13 03:16:25 2022 Chromosome 14, # of SNPs: 147
Wed Apr 13 03:16:25 2022 Chromosome 15, # of SNPs: 121
Wed Apr 13 03:16:25 2022 Chromosome 16, # of SNPs: 129
Wed Apr 13 03:16:25 2022 Chromosome 17, # of SNPs: 116
Wed Apr 13 03:16:25 2022 Chromosome 18, # of SNPs: 129
Wed Apr 13 03:16:25 2022 Chromosome 19, # of SNPs: 73
Wed Apr 13 03:16:25 2022 Chromosome 20, # of SNPs: 106
Wed Apr 13 03:16:25 2022 Chromosome 21, # of SNPs: 62
Wed Apr 13 03:16:25 2022 Chromosome 22, # of SNPs: 51
Wed Apr 13 03:16:25 2022 Chromosome 23, # of SNPs: 204
Total # of SNPs selected:4570
FUNCTION: snpgdsBED2GDS
Start file conversion from PLINK BED to SNP GDS ...
BED file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz"
SNP-major mode (Sample X SNP), 45.7K
FAM file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz"
BIM file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz"
Wed Apr 13 03:16:25 2022 (store sample id, snp id, position, and chromosome)
start writing: 60 samples, 5000 SNPs ...
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:25 2022 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
FUNCTION: snpgdsClose
FUNCTION: snpgdsCombineGeno
Create a GDS genotype file:
The new dataset consists of 10 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 20 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
10 samples, 3000 SNPs
open 't2.gds' ...
20 samples, 3000 SNPs
Concatenating samples (mapping to the first GDS file) ...
reference: 3000 SNPs (100.0%)
file 2: 0 allele flips, 0 ambiguous locus/loci
[no flip]: 3000
create 'test.gds': 30 samples, 3000 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (46.2K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (46.0K, reduced: 204B)
# of fragments: 15
Done.
Create a GDS genotype file:
The new dataset consists of 279 samples and 100 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 279 samples and 200 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
279 samples, 100 SNPs
open 't2.gds' ...
279 samples, 200 SNPs
Concatenating SNPs ...
create 'test.gds': 279 samples, 300 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (19.1K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (18.9K, reduced: 204B)
# of fragments: 15
Done.
FUNCTION: snpgdsCreateGeno
Principal Component Analysis (PCA) on genotypes:
Excluding 42 SNPs on non-autosomes
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 958
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 264760
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:25 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:25 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:16:25 2022 Done.
FUNCTION: snpgdsCreateGenoSet
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 76.12%, 545/716
Chromosome 2: 72.78%, 540/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.49%, 413/562
Chromosome 5: 76.86%, 435/566
Chromosome 6: 75.75%, 428/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.11%, 347/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.12%, 358/483
Chromosome 11: 77.85%, 348/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 76.16%, 262/344
Chromosome 14: 76.60%, 216/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 73.91%, 153/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,557 markers are selected in total.
Create a GDS genotype file:
The new dataset consists of 279 samples and 6557 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsCutTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Wed Apr 13 03:16:26 2022 0%
Dissimilarity: Wed Apr 13 03:16:27 2022 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
Create 4 groups.
FUNCTION: snpgdsDiss
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Wed Apr 13 03:16:28 2022 0%
Dissimilarity: Wed Apr 13 03:16:29 2022 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsDrawTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Wed Apr 13 03:16:30 2022 0%
Dissimilarity: Wed Apr 13 03:16:31 2022 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsEIGMIX
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:32 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:32 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:16:32 2022 Done.
FUNCTION: snpgdsErrMsg
FUNCTION: snpgdsExampleFileName
FUNCTION: snpgdsFst
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
Method: Weir & Cockerham, 1984
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
Method: Weir & Hill, 2002
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
FUNCTION: snpgdsGDS2BED
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to PLINK binary PED:
Working space: 279 samples, 8722 SNPs
Output a BIM file.
Output a BED file ...
Wed Apr 13 03:16:32 2022 0%
Wed Apr 13 03:16:32 2022 100%
Done.
FUNCTION: snpgdsGDS2Eigen
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to EIGENSOFT:
save to *.snp: 8722 snps
save to *.ind: 279 samples
Output: Wed Apr 13 03:16:32 2022 0%
Output: Wed Apr 13 03:16:33 2022 100%
Done.
FUNCTION: snpgdsGDS2PED
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Wed Apr 13 03:16:33 2022 0%
Output: Wed Apr 13 03:16:33 2022 100%
FUNCTION: snpgdsGEN2GDS
running snpgdsGEN2GDS ...
FUNCTION: snpgdsGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:33 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:33 2022 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:33 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:34 2022 Done.
FUNCTION: snpgdsGetGeno
Genotype matrix: 1000 SNPs X 279 samples
Genotype matrix: 279 samples X 1000 SNPs
FUNCTION: snpgdsHCluster
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Wed Apr 13 03:16:34 2022 0%
Dissimilarity: Wed Apr 13 03:16:35 2022 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsHWE
Keeping 716 SNPs according to chromosome 1
Excluding 160 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
FUNCTION: snpgdsIBDKING
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:36 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:36 2022 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:36 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:36 2022 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
# of families: 20, and within- and between-family relationship are estimated differently.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:37 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:37 2022 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Wed Apr 13 03:16:37 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:37 2022 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Wed Apr 13 03:16:37 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:37 2022 Done.
FUNCTION: snpgdsIBDMLE
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 30
# of SNPs: 7,142
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.31%, 403/742
Chromosome 3: 55.99%, 341/609
Chromosome 4: 56.58%, 318/562
Chromosome 5: 56.36%, 319/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 56.14%, 265/472
Chromosome 8: 51.84%, 253/488
Chromosome 9: 54.81%, 228/416
Chromosome 10: 49.90%, 241/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 54.57%, 233/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 56.03%, 158/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 53.28%, 122/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 51.72%, 60/116
4,762 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 30
# of SNPs: 250
using 1 thread
MLE IBD: the sum of all selected genotypes (0,1,2) = 7859
MLE IBD: Wed Apr 13 03:16:38 2022 0%
MLE IBD: Wed Apr 13 03:16:39 2022 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.525, sd: 0.288
MLE IBD: the sum of all selected genotypes (0,1,2) = 6545
MLE IBD: Wed Apr 13 03:16:39 2022 0%
MLE IBD: Wed Apr 13 03:16:39 2022 100%
FUNCTION: snpgdsIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 30
# of SNPs: 7,142
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.31%, 403/742
Chromosome 3: 55.99%, 341/609
Chromosome 4: 56.58%, 318/562
Chromosome 5: 56.36%, 319/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 56.14%, 265/472
Chromosome 8: 51.84%, 253/488
Chromosome 9: 54.81%, 228/416
Chromosome 10: 49.90%, 241/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 54.57%, 233/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 56.03%, 158/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 53.28%, 122/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 51.72%, 60/116
4,762 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 30
# of SNPs: 250
using 1 thread
MLE IBD: the sum of all selected genotypes (0,1,2) = 7859
MLE IBD: Wed Apr 13 03:16:39 2022 0%
MLE IBD: Wed Apr 13 03:16:40 2022 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.525, sd: 0.288
MLE IBD: the sum of all selected genotypes (0,1,2) = 6545
MLE IBD: Wed Apr 13 03:16:40 2022 0%
MLE IBD: Wed Apr 13 03:16:40 2022 100%
FUNCTION: snpgdsIBDMoM
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 702139
Wed Apr 13 03:16:40 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:40 2022 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Wed Apr 13 03:16:40 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:40 2022 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Wed Apr 13 03:16:40 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:40 2022 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 8,160
using 1 thread
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 203285
Wed Apr 13 03:16:40 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:40 2022 Done.
FUNCTION: snpgdsIBDSelection
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Wed Apr 13 03:16:41 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:41 2022 Done.
FUNCTION: snpgdsIBS
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:16:41 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:41 2022 Done.
FUNCTION: snpgdsIBSNum
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:16:41 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:41 2022 Done.
FUNCTION: snpgdsIndInb
Estimating individual inbreeding coefficients:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
FUNCTION: snpgdsIndInbCoef
FUNCTION: snpgdsIndivBeta
Individual Inbreeding and Relatedness (beta estimator):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Individual Beta: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:42 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:42 2022 Done.
FUNCTION: snpgdsLDMat
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 203
using 1 thread
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 203
using 1 thread
sliding window size: 203
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
FUNCTION: snpgdsLDpair
FUNCTION: snpgdsLDpruning
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 76.12%, 545/716
Chromosome 2: 72.78%, 540/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.49%, 413/562
Chromosome 5: 76.86%, 435/566
Chromosome 6: 75.75%, 428/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.11%, 347/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.12%, 358/483
Chromosome 11: 77.85%, 348/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 76.16%, 262/344
Chromosome 14: 76.60%, 216/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 73.91%, 153/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,557 markers are selected in total.
List of 22
$ chr1 : int [1:545] 1 2 4 5 7 10 12 14 15 16 ...
$ chr2 : int [1:540] 717 718 719 720 721 723 724 725 726 727 ...
$ chr3 : int [1:455] 1459 1460 1461 1464 1466 1468 1469 1471 1472 1473 ...
$ chr4 : int [1:413] 2068 2069 2070 2071 2072 2074 2075 2076 2077 2078 ...
$ chr5 : int [1:435] 2630 2631 2633 2635 2636 2637 2638 2640 2642 2643 ...
$ chr6 : int [1:428] 3196 3197 3198 3200 3201 3204 3205 3206 3207 3208 ...
$ chr7 : int [1:356] 3761 3762 3763 3766 3767 3768 3770 3771 3772 3773 ...
$ chr8 : int [1:347] 4233 4234 4235 4236 4237 4238 4239 4240 4241 4242 ...
$ chr9 : int [1:324] 4721 4722 4724 4727 4728 4730 4731 4732 4733 4735 ...
$ chr10: int [1:358] 5138 5139 5140 5143 5144 5145 5146 5147 5148 5149 ...
$ chr11: int [1:348] 5620 5621 5623 5624 5625 5626 5628 5629 5630 5631 ...
$ chr12: int [1:328] 6067 6068 6069 6070 6073 6074 6075 6077 6078 6079 ...
$ chr13: int [1:262] 6494 6497 6498 6499 6500 6501 6503 6505 6507 6509 ...
$ chr14: int [1:216] 6840 6841 6842 6843 6844 6845 6846 6847 6848 6850 ...
$ chr15: int [1:200] 7120 7121 7122 7124 7125 7126 7127 7128 7129 7130 ...
$ chr16: int [1:202] 7382 7383 7384 7385 7387 7388 7389 7391 7392 7394 ...
$ chr17: int [1:153] 7660 7661 7662 7663 7664 7665 7666 7667 7668 7669 ...
$ chr18: int [1:196] 7867 7868 7869 7870 7871 7872 7873 7874 7875 7877 ...
$ chr19: int [1:102] 8133 8135 8136 8137 8138 8139 8140 8141 8142 8144 ...
$ chr20: int [1:164] 8253 8254 8257 8258 8259 8260 8261 8262 8265 8266 ...
$ chr21: int [1:97] 8482 8484 8485 8486 8487 8488 8489 8490 8491 8492 ...
$ chr22: int [1:88] 8608 8609 8610 8612 8613 8614 8615 8617 8618 8619 ...
FUNCTION: snpgdsMergeGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:42 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:16:43 2022 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,400
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 951558
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:43 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:16:44 2022 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,400
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 957408
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:44 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:44 2022 Done.
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
FUNCTION: snpgdsOpen
FUNCTION: snpgdsOption
FUNCTION: snpgdsPCA
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:45 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:16:46 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:16:46 2022 Done.
FUNCTION: snpgdsPCACorr
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:46 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:46 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:16:46 2022 Done.
SNP Correlation:
# of samples: 279
# of SNPs: 9,088
using 1 thread
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Wed Apr 13 03:16:46 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:46 2022 Done.
SNP Correlation:
# of samples: 279
# of SNPs: 9,088
using 1 thread
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Wed Apr 13 03:16:47 2022
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:47 2022 Done.
FUNCTION: snpgdsPCASNPLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 8
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:47 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:47 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:16:47 2022 Done.
SNP Loading:
# of samples: 279
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:16:47 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:47 2022 Done.
FUNCTION: snpgdsPCASampLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 8
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:47 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:16:48 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:16:48 2022 Done.
SNP Loading:
# of samples: 279
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:16:48 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:48 2022 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 878146
Wed Apr 13 03:16:48 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:48 2022 Done.
FUNCTION: snpgdsPED2GDS
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Wed Apr 13 03:16:48 2022 0%
Output: Wed Apr 13 03:16:48 2022 100%
PLINK PED/MAP to GDS Format:
Import 9088 variants from 'tmp.map'
Chromosome:
1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7
716 483 447 427 344 282 262 278 207 266 120 742 229 126 116 609 562 566 565 472
8 9 X
488 416 365
Reading 'tmp.ped'
Output: 'test.gds'
Import 279 samples
Transpose the genotypic matrix ...
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 50
save to 'test.gds.tmp'
rename 'test.gds.tmp' (711.4K, reduced: 618.7K)
# of fragments: 26
FUNCTION: snpgdsPairIBD
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 93
# of SNPs: 7,077
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.67%, 465/742
Chromosome 3: 59.93%, 365/609
Chromosome 4: 64.23%, 361/562
Chromosome 5: 62.37%, 353/566
Chromosome 6: 59.82%, 338/565
Chromosome 7: 63.14%, 298/472
Chromosome 8: 57.58%, 281/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.46%, 292/483
Chromosome 11: 63.09%, 282/447
Chromosome 12: 62.76%, 268/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.83%, 180/282
Chromosome 15: 63.74%, 167/262
Chromosome 16: 62.23%, 173/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.40%, 158/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 66.38%, 152/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,420 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Wed Apr 13 03:16:49 2022 0%
MLE IBD: Wed Apr 13 03:16:50 2022 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6112
Wed Apr 13 03:16:50 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:50 2022 Done.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Wed Apr 13 03:16:50 2022 0%
MLE IBD: Wed Apr 13 03:16:51 2022 100%
Genotype matrix: 250 SNPs X 25 samples
[1] -370.7482
[1] -402.2141
[1] -383.7897
[1] -377.9084
[1] -381.3139
[1] -397.5581
[1] -378.3344
[1] -370.703
[1] -376.103
[1] -377.7911
[1] -375.5425
[1] -373.13
[1] -383.6992
[1] -393.5194
[1] -371.9843
[1] -369.6468
[1] -374.5139
[1] -377.841
[1] -387.5622
[1] -377.1646
[1] -377.4659
[1] -375.2204
[1] -372.0639
[1] -379.816
FUNCTION: snpgdsPairIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 93
# of SNPs: 7,077
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.67%, 465/742
Chromosome 3: 59.93%, 365/609
Chromosome 4: 64.23%, 361/562
Chromosome 5: 62.37%, 353/566
Chromosome 6: 59.82%, 338/565
Chromosome 7: 63.14%, 298/472
Chromosome 8: 57.58%, 281/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.46%, 292/483
Chromosome 11: 63.09%, 282/447
Chromosome 12: 62.76%, 268/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.83%, 180/282
Chromosome 15: 63.74%, 167/262
Chromosome 16: 62.23%, 173/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.40%, 158/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 66.38%, 152/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,420 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Wed Apr 13 03:16:51 2022 0%
MLE IBD: Wed Apr 13 03:16:52 2022 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6112
Wed Apr 13 03:16:52 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:52 2022 Done.
Genotype matrix: 250 SNPs X 25 samples
[1] -370.7482
[1] -402.2141
[1] -383.7897
[1] -377.9084
[1] -381.3139
[1] -397.5581
[1] -378.3344
[1] -370.703
[1] -376.103
[1] -377.7911
[1] -375.5425
[1] -373.13
[1] -383.6992
[1] -393.5194
[1] -371.9843
[1] -369.6468
[1] -374.5139
[1] -377.841
[1] -387.5622
[1] -377.1646
[1] -377.4659
[1] -375.2204
[1] -372.0639
[1] -379.816
FUNCTION: snpgdsPairScore
Excluding 365 SNPs on non-autosomes
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score :'data.frame': 60 obs. of 5 variables:
..$ Avg : num [1:60] 1.72 1.73 1.71 1.72 1.73 ...
..$ SD : num [1:60] 0.452 0.443 0.457 0.45 0.443 ...
..$ Num : int [1:60] 8684 8627 8669 8637 8682 8634 8654 8678 8680 8679 ...
..$ Sample1: chr [1:60] "NA19139" "NA10847" "NA18515" "NA19129" ...
..$ Sample2: chr [1:60] "NA19138" "NA12146" "NA18516" "NA19128" ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score :'data.frame': 60 obs. of 5 variables:
..$ Avg : num [1:60] 0.999 1 1 1 1 ...
..$ SD : num [1:60] 0.024 0 0.0186 0.0215 0.0215 ...
..$ Num : int [1:60] 8684 8627 8669 8637 8682 8634 8654 8678 8680 8679 ...
..$ Sample1: chr [1:60] "NA19139" "NA10847" "NA18515" "NA19129" ...
..$ Sample2: chr [1:60] "NA19138" "NA12146" "NA18516" "NA19128" ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score : num [1:3, 1:8723] 1.75 0.437 60 1.583 0.497 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:3] "Avg" "SD" "Num"
.. ..$ : NULL
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score : int [1:60, 1:8723] 1 1 2 2 2 2 2 1 2 2 ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Output: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\tmp.gds
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
FUNCTION: snpgdsSNPList
FUNCTION: snpgdsSNPListClass
FUNCTION: snpgdsSNPListIntersect
FUNCTION: snpgdsSNPRateFreq
FUNCTION: snpgdsSampMissRate
FUNCTION: snpgdsSelectSNP
Excluding 365 SNPs on non-autosomes
Excluding 1,221 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.95)
FUNCTION: snpgdsSlidingWindow
Sliding Window Analysis:
Excluding 8 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 9,080
using 1 thread
window size: 500000, shift: 100000 (basepair)
Chromosome Set: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23
Wed Apr 13 03:16:53 2022, Chromosome 1 (716 SNPs), 2448 windows
Wed Apr 13 03:16:53 2022, Chromosome 2 (742 SNPs), 2416 windows
Wed Apr 13 03:16:53 2022, Chromosome 3 (609 SNPs), 1985 windows
Wed Apr 13 03:16:53 2022, Chromosome 4 (562 SNPs), 1894 windows
Wed Apr 13 03:16:53 2022, Chromosome 5 (566 SNPs), 1797 windows
Wed Apr 13 03:16:53 2022, Chromosome 6 (565 SNPs), 1694 windows
Wed Apr 13 03:16:54 2022, Chromosome 7 (472 SNPs), 1573 windows
Wed Apr 13 03:16:54 2022, Chromosome 8 (488 SNPs), 1445 windows
Wed Apr 13 03:16:54 2022, Chromosome 9 (416 SNPs), 1393 windows
Wed Apr 13 03:16:54 2022, Chromosome 10 (483 SNPs), 1343 windows
Wed Apr 13 03:16:54 2022, Chromosome 11 (447 SNPs), 1338 windows
Wed Apr 13 03:16:54 2022, Chromosome 12 (427 SNPs), 1316 windows
Wed Apr 13 03:16:54 2022, Chromosome 13 (344 SNPs), 948 windows
Wed Apr 13 03:16:54 2022, Chromosome 14 (281 SNPs), 847 windows
Wed Apr 13 03:16:54 2022, Chromosome 15 (262 SNPs), 774 windows
Wed Apr 13 03:16:54 2022, Chromosome 16 (278 SNPs), 873 windows
Wed Apr 13 03:16:54 2022, Chromosome 17 (207 SNPs), 773 windows
Wed Apr 13 03:16:54 2022, Chromosome 18 (266 SNPs), 753 windows
Wed Apr 13 03:16:54 2022, Chromosome 19 (120 SNPs), 627 windows
Wed Apr 13 03:16:54 2022, Chromosome 20 (229 SNPs), 602 windows
Wed Apr 13 03:16:54 2022, Chromosome 21 (126 SNPs), 311 windows
Wed Apr 13 03:16:54 2022, Chromosome 22 (116 SNPs), 312 windows
Wed Apr 13 03:16:54 2022, Chromosome 23 (358 SNPs), 1507 windows
Wed Apr 13 03:16:54 2022 Done.
FUNCTION: snpgdsSummary
The file name: C:\Users\biocbuild\bbs-3.14-bioc\R\library\SNPRelate\extdata\hapmap_geno.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsTranspose
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
SNP genotypes: 279 samples, 9088 SNPs
Genotype matrix is being transposed ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 28
save to 'test.gds.tmp'
rename 'test.gds.tmp' (709.6K, reduced: 619.1K)
# of fragments: 26
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in individual-major mode (SNP X Sample).
FUNCTION: snpgdsVCF2GDS
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start file conversion from VCF to SNP GDS ...
Method: extracting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test1.gds' (2.9K)
# of fragments: 46
save to 'test1.gds.tmp'
rename 'test1.gds.tmp' (2.6K, reduced: 312B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start file conversion from VCF to SNP GDS ...
Method: extracting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
SNP genotypes: 3 samples, 2 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test2.gds' (3.0K)
# of fragments: 48
save to 'test2.gds.tmp'
rename 'test2.gds.tmp' (2.6K, reduced: 417B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in individual-major mode (SNP X Sample).
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
SNP genotypes: 3 samples, 5 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test3.gds' (3.1K)
# of fragments: 48
save to 'test3.gds.tmp'
rename 'test3.gds.tmp' (2.7K, reduced: 419B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in individual-major mode (SNP X Sample).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test4.gds' (3.0K)
# of fragments: 46
save to 'test4.gds.tmp'
rename 'test4.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test5.gds' (3.0K)
# of fragments: 46
save to 'test5.gds.tmp'
rename 'test5.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., T/A,G).
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test5.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
FUNCTION: snpgdsVCF2GDS_R
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Wed Apr 13 03:16:54 2022 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Wed Apr 13 03:16:54 2022 Done.
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Wed Apr 13 03:16:54 2022 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Wed Apr 13 03:16:55 2022 Done.
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Wed Apr 13 03:16:55 2022 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
Wed Apr 13 03:16:55 2022 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Wed Apr 13 03:16:55 2022 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
Wed Apr 13 03:16:55 2022 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_i386\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 1 thread
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Wed Apr 13 03:16:57 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:57 2022 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 1 thread
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Wed Apr 13 03:16:57 2022
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:57 2022 Done.
SNP Loading:
# of samples: 90
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Wed Apr 13 03:16:57 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:57 2022 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Wed Apr 13 03:16:57 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:57 2022 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 2 threads
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Wed Apr 13 03:16:57 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:57 2022 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 2 threads
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Wed Apr 13 03:16:57 2022
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:57 2022 Done.
SNP Loading:
# of samples: 90
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Wed Apr 13 03:16:57 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:57 2022 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Wed Apr 13 03:16:57 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:16:57 2022 Done.
RUNIT TEST PROTOCOL -- Wed Apr 13 03:16:58 2022
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
SNPRelate RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
43.79 2.32 45.98
|
SNPRelate.Rcheck/tests_x64/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("SNPRelate")
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Genetic Relationship Matrix (GRM, GCTA):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 1,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:16:59 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:00 2022 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 2,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:00 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:17:01 2022 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:01 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:01 2022 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:02 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:02 2022 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 1,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:02 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:03 2022 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 2,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:03 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:04 2022 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:04 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:17:05 2022 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Writing ...
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:05 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:05 2022 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 1,000
using 1 thread
method: covariance
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 1,000
using 1 thread
method: correlation
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
FUNCTION: SNPGDSFileClass
FUNCTION: SNPRelate-package
Start file conversion from PLINK BED to SNP GDS ...
BED file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz"
SNP-major mode (Sample X SNP), 45.7K
FAM file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz"
BIM file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz"
Wed Apr 13 03:17:08 2022 (store sample id, snp id, position, and chromosome)
start writing: 60 samples, 5000 SNPs ...
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:08 2022 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
Principal Component Analysis (PCA) on genotypes:
Excluding 203 SNPs on non-autosomes
Excluding 28 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 60
# of SNPs: 4,769
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 124273
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:08 2022 (internal increment: 53996)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:08 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:17:08 2022 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:17:08 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:08 2022 Done.
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:17:09 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:17:10 2022 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 200
using 1 thread
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 55417
FUNCTION: hapmap_geno
FUNCTION: snpgdsAdmixPlot
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:10 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:17:11 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:17:11 2022 Done.
FUNCTION: snpgdsAdmixProp
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:11 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:11 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:17:11 2022 Done.
FUNCTION: snpgdsAlleleSwitch
Strand-switching at 50 SNP locus/loci.
Unable to determine switching at 10 SNP locus/loci.
FUNCTION: snpgdsApartSelection
Wed Apr 13 03:17:11 2022 Chromosome 1, # of SNPs: 367
Wed Apr 13 03:17:11 2022 Chromosome 2, # of SNPs: 367
Wed Apr 13 03:17:11 2022 Chromosome 3, # of SNPs: 317
Wed Apr 13 03:17:11 2022 Chromosome 4, # of SNPs: 295
Wed Apr 13 03:17:11 2022 Chromosome 5, # of SNPs: 295
Wed Apr 13 03:17:11 2022 Chromosome 6, # of SNPs: 283
Wed Apr 13 03:17:11 2022 Chromosome 7, # of SNPs: 245
Wed Apr 13 03:17:11 2022 Chromosome 8, # of SNPs: 234
Wed Apr 13 03:17:11 2022 Chromosome 9, # of SNPs: 202
Wed Apr 13 03:17:11 2022 Chromosome 10, # of SNPs: 224
Wed Apr 13 03:17:11 2022 Chromosome 11, # of SNPs: 223
Wed Apr 13 03:17:11 2022 Chromosome 12, # of SNPs: 208
Wed Apr 13 03:17:11 2022 Chromosome 13, # of SNPs: 172
Wed Apr 13 03:17:11 2022 Chromosome 14, # of SNPs: 147
Wed Apr 13 03:17:11 2022 Chromosome 15, # of SNPs: 121
Wed Apr 13 03:17:11 2022 Chromosome 16, # of SNPs: 129
Wed Apr 13 03:17:11 2022 Chromosome 17, # of SNPs: 116
Wed Apr 13 03:17:11 2022 Chromosome 18, # of SNPs: 129
Wed Apr 13 03:17:11 2022 Chromosome 19, # of SNPs: 73
Wed Apr 13 03:17:11 2022 Chromosome 20, # of SNPs: 106
Wed Apr 13 03:17:11 2022 Chromosome 21, # of SNPs: 62
Wed Apr 13 03:17:11 2022 Chromosome 22, # of SNPs: 51
Wed Apr 13 03:17:11 2022 Chromosome 23, # of SNPs: 204
Total # of SNPs selected:4570
FUNCTION: snpgdsBED2GDS
Start file conversion from PLINK BED to SNP GDS ...
BED file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz"
SNP-major mode (Sample X SNP), 45.7K
FAM file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz"
BIM file: "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz"
Wed Apr 13 03:17:11 2022 (store sample id, snp id, position, and chromosome)
start writing: 60 samples, 5000 SNPs ...
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:11 2022 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
FUNCTION: snpgdsClose
FUNCTION: snpgdsCombineGeno
Create a GDS genotype file:
The new dataset consists of 10 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 20 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
10 samples, 3000 SNPs
open 't2.gds' ...
20 samples, 3000 SNPs
Concatenating samples (mapping to the first GDS file) ...
reference: 3000 SNPs (100.0%)
file 2: 0 allele flips, 0 ambiguous locus/loci
[no flip]: 3000
create 'test.gds': 30 samples, 3000 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (46.2K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (46.0K, reduced: 204B)
# of fragments: 15
Done.
Create a GDS genotype file:
The new dataset consists of 279 samples and 100 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 279 samples and 200 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
279 samples, 100 SNPs
open 't2.gds' ...
279 samples, 200 SNPs
Concatenating SNPs ...
create 'test.gds': 279 samples, 300 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (19.1K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (18.9K, reduced: 204B)
# of fragments: 15
Done.
FUNCTION: snpgdsCreateGeno
Principal Component Analysis (PCA) on genotypes:
Excluding 42 SNPs on non-autosomes
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 958
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 264760
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:12 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:12 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:17:12 2022 Done.
FUNCTION: snpgdsCreateGenoSet
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 76.12%, 545/716
Chromosome 2: 72.78%, 540/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.49%, 413/562
Chromosome 5: 76.86%, 435/566
Chromosome 6: 75.75%, 428/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.11%, 347/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.12%, 358/483
Chromosome 11: 77.85%, 348/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 76.16%, 262/344
Chromosome 14: 76.60%, 216/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 73.91%, 153/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,557 markers are selected in total.
Create a GDS genotype file:
The new dataset consists of 279 samples and 6557 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsCutTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Wed Apr 13 03:17:12 2022 0%
Dissimilarity: Wed Apr 13 03:17:13 2022 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
Create 4 groups.
FUNCTION: snpgdsDiss
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Wed Apr 13 03:17:14 2022 0%
Dissimilarity: Wed Apr 13 03:17:16 2022 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsDrawTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Wed Apr 13 03:17:16 2022 0%
Dissimilarity: Wed Apr 13 03:17:18 2022 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsEIGMIX
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:18 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:18 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:17:18 2022 Done.
FUNCTION: snpgdsErrMsg
FUNCTION: snpgdsExampleFileName
FUNCTION: snpgdsFst
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
Method: Weir & Cockerham, 1984
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
Method: Weir & Hill, 2002
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
FUNCTION: snpgdsGDS2BED
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to PLINK binary PED:
Working space: 279 samples, 8722 SNPs
Output a BIM file.
Output a BED file ...
Wed Apr 13 03:17:19 2022 0%
Wed Apr 13 03:17:19 2022 100%
Done.
FUNCTION: snpgdsGDS2Eigen
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to EIGENSOFT:
save to *.snp: 8722 snps
save to *.ind: 279 samples
Output: Wed Apr 13 03:17:19 2022 0%
Output: Wed Apr 13 03:17:19 2022 100%
Done.
FUNCTION: snpgdsGDS2PED
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Wed Apr 13 03:17:19 2022 0%
Output: Wed Apr 13 03:17:19 2022 100%
FUNCTION: snpgdsGEN2GDS
running snpgdsGEN2GDS ...
FUNCTION: snpgdsGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:19 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:19 2022 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:20 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:20 2022 Done.
FUNCTION: snpgdsGetGeno
Genotype matrix: 1000 SNPs X 279 samples
Genotype matrix: 279 samples X 1000 SNPs
FUNCTION: snpgdsHCluster
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Wed Apr 13 03:17:20 2022 0%
Dissimilarity: Wed Apr 13 03:17:21 2022 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsHWE
Keeping 716 SNPs according to chromosome 1
Excluding 160 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
FUNCTION: snpgdsIBDKING
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:22 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:22 2022 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:22 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:22 2022 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
# of families: 20, and within- and between-family relationship are estimated differently.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:23 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:23 2022 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Wed Apr 13 03:17:23 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:23 2022 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Wed Apr 13 03:17:23 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:23 2022 Done.
FUNCTION: snpgdsIBDMLE
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 30
# of SNPs: 7,142
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.31%, 403/742
Chromosome 3: 55.99%, 341/609
Chromosome 4: 56.58%, 318/562
Chromosome 5: 56.36%, 319/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 56.14%, 265/472
Chromosome 8: 51.84%, 253/488
Chromosome 9: 54.81%, 228/416
Chromosome 10: 49.90%, 241/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 54.57%, 233/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 56.03%, 158/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 53.28%, 122/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 51.72%, 60/116
4,762 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 30
# of SNPs: 250
using 1 thread
MLE IBD: the sum of all selected genotypes (0,1,2) = 7859
MLE IBD: Wed Apr 13 03:17:23 2022 0%
MLE IBD: Wed Apr 13 03:17:25 2022 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.525, sd: 0.288
MLE IBD: the sum of all selected genotypes (0,1,2) = 6545
MLE IBD: Wed Apr 13 03:17:25 2022 0%
MLE IBD: Wed Apr 13 03:17:25 2022 100%
FUNCTION: snpgdsIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 30
# of SNPs: 7,142
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.31%, 403/742
Chromosome 3: 55.99%, 341/609
Chromosome 4: 56.58%, 318/562
Chromosome 5: 56.36%, 319/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 56.14%, 265/472
Chromosome 8: 51.84%, 253/488
Chromosome 9: 54.81%, 228/416
Chromosome 10: 49.90%, 241/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 54.57%, 233/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 56.03%, 158/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 53.28%, 122/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 51.72%, 60/116
4,762 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 30
# of SNPs: 250
using 1 thread
MLE IBD: the sum of all selected genotypes (0,1,2) = 7859
MLE IBD: Wed Apr 13 03:17:25 2022 0%
MLE IBD: Wed Apr 13 03:17:26 2022 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.525, sd: 0.288
MLE IBD: the sum of all selected genotypes (0,1,2) = 6545
MLE IBD: Wed Apr 13 03:17:26 2022 0%
MLE IBD: Wed Apr 13 03:17:26 2022 100%
FUNCTION: snpgdsIBDMoM
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 702139
Wed Apr 13 03:17:26 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:26 2022 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Wed Apr 13 03:17:26 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:26 2022 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Wed Apr 13 03:17:27 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:27 2022 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 8,160
using 1 thread
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 203285
Wed Apr 13 03:17:27 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:27 2022 Done.
FUNCTION: snpgdsIBDSelection
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Wed Apr 13 03:17:27 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:27 2022 Done.
FUNCTION: snpgdsIBS
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:17:27 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:27 2022 Done.
FUNCTION: snpgdsIBSNum
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:17:28 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:28 2022 Done.
FUNCTION: snpgdsIndInb
Estimating individual inbreeding coefficients:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
FUNCTION: snpgdsIndInbCoef
FUNCTION: snpgdsIndivBeta
Individual Inbreeding and Relatedness (beta estimator):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Individual Beta: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:29 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:29 2022 Done.
FUNCTION: snpgdsLDMat
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 203
using 1 thread
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 203
using 1 thread
sliding window size: 203
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
FUNCTION: snpgdsLDpair
FUNCTION: snpgdsLDpruning
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 76.12%, 545/716
Chromosome 2: 72.78%, 540/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.49%, 413/562
Chromosome 5: 76.86%, 435/566
Chromosome 6: 75.75%, 428/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.11%, 347/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.12%, 358/483
Chromosome 11: 77.85%, 348/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 76.16%, 262/344
Chromosome 14: 76.60%, 216/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 73.91%, 153/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,557 markers are selected in total.
List of 22
$ chr1 : int [1:545] 1 2 4 5 7 10 12 14 15 16 ...
$ chr2 : int [1:540] 717 718 719 720 721 723 724 725 726 727 ...
$ chr3 : int [1:455] 1459 1460 1461 1464 1466 1468 1469 1471 1472 1473 ...
$ chr4 : int [1:413] 2068 2069 2070 2071 2072 2074 2075 2076 2077 2078 ...
$ chr5 : int [1:435] 2630 2631 2633 2635 2636 2637 2638 2640 2642 2643 ...
$ chr6 : int [1:428] 3196 3197 3198 3200 3201 3204 3205 3206 3207 3208 ...
$ chr7 : int [1:356] 3761 3762 3763 3766 3767 3768 3770 3771 3772 3773 ...
$ chr8 : int [1:347] 4233 4234 4235 4236 4237 4238 4239 4240 4241 4242 ...
$ chr9 : int [1:324] 4721 4722 4724 4727 4728 4730 4731 4732 4733 4735 ...
$ chr10: int [1:358] 5138 5139 5140 5143 5144 5145 5146 5147 5148 5149 ...
$ chr11: int [1:348] 5620 5621 5623 5624 5625 5626 5628 5629 5630 5631 ...
$ chr12: int [1:328] 6067 6068 6069 6070 6073 6074 6075 6077 6078 6079 ...
$ chr13: int [1:262] 6494 6497 6498 6499 6500 6501 6503 6505 6507 6509 ...
$ chr14: int [1:216] 6840 6841 6842 6843 6844 6845 6846 6847 6848 6850 ...
$ chr15: int [1:200] 7120 7121 7122 7124 7125 7126 7127 7128 7129 7130 ...
$ chr16: int [1:202] 7382 7383 7384 7385 7387 7388 7389 7391 7392 7394 ...
$ chr17: int [1:153] 7660 7661 7662 7663 7664 7665 7666 7667 7668 7669 ...
$ chr18: int [1:196] 7867 7868 7869 7870 7871 7872 7873 7874 7875 7877 ...
$ chr19: int [1:102] 8133 8135 8136 8137 8138 8139 8140 8141 8142 8144 ...
$ chr20: int [1:164] 8253 8254 8257 8258 8259 8260 8261 8262 8265 8266 ...
$ chr21: int [1:97] 8482 8484 8485 8486 8487 8488 8489 8490 8491 8492 ...
$ chr22: int [1:88] 8608 8609 8610 8612 8613 8614 8615 8617 8618 8619 ...
FUNCTION: snpgdsMergeGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:29 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:17:30 2022 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,400
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 951558
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:30 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:30 2022 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,400
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 957408
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:30 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:17:31 2022 Done.
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
FUNCTION: snpgdsOpen
FUNCTION: snpgdsOption
FUNCTION: snpgdsPCA
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:31 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:17:32 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:17:32 2022 Done.
FUNCTION: snpgdsPCACorr
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:32 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:32 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:17:32 2022 Done.
SNP Correlation:
# of samples: 279
# of SNPs: 9,088
using 1 thread
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Wed Apr 13 03:17:32 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:32 2022 Done.
SNP Correlation:
# of samples: 279
# of SNPs: 9,088
using 1 thread
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Wed Apr 13 03:17:32 2022
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Wed Apr 13 03:17:33 2022 Done.
FUNCTION: snpgdsPCASNPLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 8
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:33 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:33 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:17:33 2022 Done.
SNP Loading:
# of samples: 279
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:17:33 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:33 2022 Done.
FUNCTION: snpgdsPCASampLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 8
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Wed Apr 13 03:17:33 2022 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:33 2022 Begin (eigenvalues and eigenvectors)
Wed Apr 13 03:17:33 2022 Done.
SNP Loading:
# of samples: 279
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Wed Apr 13 03:17:33 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:33 2022 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 878146
Wed Apr 13 03:17:33 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:33 2022 Done.
FUNCTION: snpgdsPED2GDS
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Wed Apr 13 03:17:34 2022 0%
Output: Wed Apr 13 03:17:34 2022 100%
PLINK PED/MAP to GDS Format:
Import 9088 variants from 'tmp.map'
Chromosome:
1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7
716 483 447 427 344 282 262 278 207 266 120 742 229 126 116 609 562 566 565 472
8 9 X
488 416 365
Reading 'tmp.ped'
Output: 'test.gds'
Import 279 samples
Transpose the genotypic matrix ...
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 50
save to 'test.gds.tmp'
rename 'test.gds.tmp' (711.4K, reduced: 618.7K)
# of fragments: 26
FUNCTION: snpgdsPairIBD
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 93
# of SNPs: 7,077
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.67%, 465/742
Chromosome 3: 59.93%, 365/609
Chromosome 4: 64.23%, 361/562
Chromosome 5: 62.37%, 353/566
Chromosome 6: 59.82%, 338/565
Chromosome 7: 63.14%, 298/472
Chromosome 8: 57.58%, 281/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.46%, 292/483
Chromosome 11: 63.09%, 282/447
Chromosome 12: 62.76%, 268/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.83%, 180/282
Chromosome 15: 63.74%, 167/262
Chromosome 16: 62.23%, 173/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.40%, 158/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 66.38%, 152/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,420 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Wed Apr 13 03:17:35 2022 0%
MLE IBD: Wed Apr 13 03:17:36 2022 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6112
Wed Apr 13 03:17:36 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:36 2022 Done.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Wed Apr 13 03:17:36 2022 0%
MLE IBD: Wed Apr 13 03:17:37 2022 100%
Genotype matrix: 250 SNPs X 25 samples
[1] -370.7482
[1] -402.2141
[1] -383.7897
[1] -377.9084
[1] -381.3139
[1] -397.5581
[1] -378.3344
[1] -370.703
[1] -376.103
[1] -377.7911
[1] -375.5425
[1] -373.13
[1] -383.6992
[1] -393.5194
[1] -371.9843
[1] -369.6468
[1] -374.5139
[1] -377.841
[1] -387.5622
[1] -377.1646
[1] -377.4659
[1] -375.2204
[1] -372.0639
[1] -379.816
FUNCTION: snpgdsPairIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 93
# of SNPs: 7,077
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.67%, 465/742
Chromosome 3: 59.93%, 365/609
Chromosome 4: 64.23%, 361/562
Chromosome 5: 62.37%, 353/566
Chromosome 6: 59.82%, 338/565
Chromosome 7: 63.14%, 298/472
Chromosome 8: 57.58%, 281/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.46%, 292/483
Chromosome 11: 63.09%, 282/447
Chromosome 12: 62.76%, 268/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.83%, 180/282
Chromosome 15: 63.74%, 167/262
Chromosome 16: 62.23%, 173/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.40%, 158/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 66.38%, 152/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,420 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Wed Apr 13 03:17:37 2022 0%
MLE IBD: Wed Apr 13 03:17:38 2022 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6112
Wed Apr 13 03:17:38 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:38 2022 Done.
Genotype matrix: 250 SNPs X 25 samples
[1] -370.7482
[1] -402.2141
[1] -383.7897
[1] -377.9084
[1] -381.3139
[1] -397.5581
[1] -378.3344
[1] -370.703
[1] -376.103
[1] -377.7911
[1] -375.5425
[1] -373.13
[1] -383.6992
[1] -393.5194
[1] -371.9843
[1] -369.6468
[1] -374.5139
[1] -377.841
[1] -387.5622
[1] -377.1646
[1] -377.4659
[1] -375.2204
[1] -372.0639
[1] -379.816
FUNCTION: snpgdsPairScore
Excluding 365 SNPs on non-autosomes
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score :'data.frame': 60 obs. of 5 variables:
..$ Avg : num [1:60] 1.72 1.73 1.71 1.72 1.73 ...
..$ SD : num [1:60] 0.452 0.443 0.457 0.45 0.443 ...
..$ Num : int [1:60] 8684 8627 8669 8637 8682 8634 8654 8678 8680 8679 ...
..$ Sample1: chr [1:60] "NA19139" "NA10847" "NA18515" "NA19129" ...
..$ Sample2: chr [1:60] "NA19138" "NA12146" "NA18516" "NA19128" ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score :'data.frame': 60 obs. of 5 variables:
..$ Avg : num [1:60] 0.999 1 1 1 1 ...
..$ SD : num [1:60] 0.024 0 0.0186 0.0215 0.0215 ...
..$ Num : int [1:60] 8684 8627 8669 8637 8682 8634 8654 8678 8680 8679 ...
..$ Sample1: chr [1:60] "NA19139" "NA10847" "NA18515" "NA19129" ...
..$ Sample2: chr [1:60] "NA19138" "NA12146" "NA18516" "NA19128" ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score : num [1:3, 1:8723] 1.75 0.437 60 1.583 0.497 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:3] "Avg" "SD" "Num"
.. ..$ : NULL
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score : int [1:60, 1:8723] 1 1 2 2 2 2 2 1 2 2 ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Output: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\tmp.gds
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
FUNCTION: snpgdsSNPList
FUNCTION: snpgdsSNPListClass
FUNCTION: snpgdsSNPListIntersect
FUNCTION: snpgdsSNPRateFreq
FUNCTION: snpgdsSampMissRate
FUNCTION: snpgdsSelectSNP
Excluding 365 SNPs on non-autosomes
Excluding 1,221 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.95)
FUNCTION: snpgdsSlidingWindow
Sliding Window Analysis:
Excluding 8 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 9,080
using 1 thread
window size: 500000, shift: 100000 (basepair)
Chromosome Set: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23
Wed Apr 13 03:17:39 2022, Chromosome 1 (716 SNPs), 2448 windows
Wed Apr 13 03:17:39 2022, Chromosome 2 (742 SNPs), 2416 windows
Wed Apr 13 03:17:39 2022, Chromosome 3 (609 SNPs), 1985 windows
Wed Apr 13 03:17:39 2022, Chromosome 4 (562 SNPs), 1894 windows
Wed Apr 13 03:17:39 2022, Chromosome 5 (566 SNPs), 1797 windows
Wed Apr 13 03:17:39 2022, Chromosome 6 (565 SNPs), 1694 windows
Wed Apr 13 03:17:39 2022, Chromosome 7 (472 SNPs), 1573 windows
Wed Apr 13 03:17:39 2022, Chromosome 8 (488 SNPs), 1445 windows
Wed Apr 13 03:17:39 2022, Chromosome 9 (416 SNPs), 1393 windows
Wed Apr 13 03:17:39 2022, Chromosome 10 (483 SNPs), 1343 windows
Wed Apr 13 03:17:39 2022, Chromosome 11 (447 SNPs), 1338 windows
Wed Apr 13 03:17:39 2022, Chromosome 12 (427 SNPs), 1316 windows
Wed Apr 13 03:17:39 2022, Chromosome 13 (344 SNPs), 948 windows
Wed Apr 13 03:17:39 2022, Chromosome 14 (281 SNPs), 847 windows
Wed Apr 13 03:17:39 2022, Chromosome 15 (262 SNPs), 774 windows
Wed Apr 13 03:17:39 2022, Chromosome 16 (278 SNPs), 873 windows
Wed Apr 13 03:17:39 2022, Chromosome 17 (207 SNPs), 773 windows
Wed Apr 13 03:17:39 2022, Chromosome 18 (266 SNPs), 753 windows
Wed Apr 13 03:17:39 2022, Chromosome 19 (120 SNPs), 627 windows
Wed Apr 13 03:17:39 2022, Chromosome 20 (229 SNPs), 602 windows
Wed Apr 13 03:17:39 2022, Chromosome 21 (126 SNPs), 311 windows
Wed Apr 13 03:17:39 2022, Chromosome 22 (116 SNPs), 312 windows
Wed Apr 13 03:17:39 2022, Chromosome 23 (358 SNPs), 1507 windows
Wed Apr 13 03:17:39 2022 Done.
FUNCTION: snpgdsSummary
The file name: C:\Users\biocbuild\bbs-3.14-bioc\R\library\SNPRelate\extdata\hapmap_geno.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsTranspose
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
SNP genotypes: 279 samples, 9088 SNPs
Genotype matrix is being transposed ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 28
save to 'test.gds.tmp'
rename 'test.gds.tmp' (709.6K, reduced: 619.1K)
# of fragments: 26
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in individual-major mode (SNP X Sample).
FUNCTION: snpgdsVCF2GDS
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start file conversion from VCF to SNP GDS ...
Method: extracting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test1.gds' (2.9K)
# of fragments: 46
save to 'test1.gds.tmp'
rename 'test1.gds.tmp' (2.6K, reduced: 312B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start file conversion from VCF to SNP GDS ...
Method: extracting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
SNP genotypes: 3 samples, 2 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test2.gds' (3.0K)
# of fragments: 48
save to 'test2.gds.tmp'
rename 'test2.gds.tmp' (2.6K, reduced: 417B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in individual-major mode (SNP X Sample).
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
SNP genotypes: 3 samples, 5 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test3.gds' (3.1K)
# of fragments: 48
save to 'test3.gds.tmp'
rename 'test3.gds.tmp' (2.7K, reduced: 419B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in individual-major mode (SNP X Sample).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test4.gds' (3.0K)
# of fragments: 46
save to 'test4.gds.tmp'
rename 'test4.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test5.gds' (3.0K)
# of fragments: 46
save to 'test5.gds.tmp'
rename 'test5.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., T/A,G).
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test5.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
FUNCTION: snpgdsVCF2GDS_R
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Wed Apr 13 03:17:40 2022 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Wed Apr 13 03:17:40 2022 Done.
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Wed Apr 13 03:17:40 2022 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Wed Apr 13 03:17:40 2022 Done.
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Wed Apr 13 03:17:40 2022 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
Wed Apr 13 03:17:40 2022 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Wed Apr 13 03:17:40 2022 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/SNPRelate/extdata/sequence.vcf
Wed Apr 13 03:17:40 2022 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.14-bioc\meat\SNPRelate.Rcheck\tests_x64\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 1 thread
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Wed Apr 13 03:17:41 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:41 2022 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 1 thread
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Wed Apr 13 03:17:41 2022
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:41 2022 Done.
SNP Loading:
# of samples: 90
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Wed Apr 13 03:17:41 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:41 2022 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Wed Apr 13 03:17:41 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:41 2022 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 2 threads
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Wed Apr 13 03:17:42 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:42 2022 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 2 threads
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Wed Apr 13 03:17:42 2022
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:42 2022 Done.
SNP Loading:
# of samples: 90
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Wed Apr 13 03:17:42 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:42 2022 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Wed Apr 13 03:17:42 2022 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Wed Apr 13 03:17:42 2022 Done.
RUNIT TEST PROTOCOL -- Wed Apr 13 03:17:42 2022
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
SNPRelate RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
41.93 2.06 43.87
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SNPRelate.Rcheck/examples_i386/SNPRelate-Ex.timings
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SNPRelate.Rcheck/examples_x64/SNPRelate-Ex.timings
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