Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:46 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 |
Package 1974/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SNPRelate 1.39.0 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the SNPRelate package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: SNPRelate |
Version: 1.39.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SNPRelate.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SNPRelate_1.39.0.tar.gz |
StartedAt: 2024-08-21 09:22:31 -0000 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 09:26:54 -0000 (Wed, 21 Aug 2024) |
EllapsedTime: 262.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SNPRelate.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:SNPRelate.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SNPRelate_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SNPRelate/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SNPRelate’ version ‘1.39.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SNPRelate’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: libs 4.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... NOTE checkRd: (-1) snpgdsGRM.Rd:52: Lost braces; missing escapes or markup? 52 | $G_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for | ^ checkRd: (-1) snpgdsGRM.Rd:52: Lost braces; missing escapes or markup? 52 | $G_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for | ^ checkRd: (-1) snpgdsGRM.Rd:52: Lost braces; missing escapes or markup? 52 | $G_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for | ^ checkRd: (-1) snpgdsGRM.Rd:56: Lost braces; missing escapes or markup? 56 | $G_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for | ^ checkRd: (-1) snpgdsGRM.Rd:56: Lost braces; missing escapes or markup? 56 | $G_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for | ^ checkRd: (-1) snpgdsGRM.Rd:56: Lost braces; missing escapes or markup? 56 | $G_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for | ^ checkRd: (-1) snpgdsGRM.Rd:62: Lost braces; missing escapes or markup? 62 | $G_{ij} = [sum_l (g_{il} - 2*p_l)*(g_{jl} - 2*p_l)] / [sum_l 2*p_l*(1 - p_l)]$ | ^ checkRd: (-1) snpgdsGRM.Rd:62: Lost braces; missing escapes or markup? 62 | $G_{ij} = [sum_l (g_{il} - 2*p_l)*(g_{jl} - 2*p_l)] / [sum_l 2*p_l*(1 - p_l)]$ | ^ checkRd: (-1) snpgdsGRM.Rd:62: Lost braces; missing escapes or markup? 62 | $G_{ij} = [sum_l (g_{il} - 2*p_l)*(g_{jl} - 2*p_l)] / [sum_l 2*p_l*(1 - p_l)]$ | ^ checkRd: (-1) snpgdsGRM.Rd:66: Lost braces; missing escapes or markup? 66 | beta-based GRM is $grm_{ij} = 2 * (beta_{ij} - beta_{min}) / (1 - beta_{min})$ for $i!=j$, | ^ checkRd: (-1) snpgdsGRM.Rd:66: Lost braces; missing escapes or markup? 66 | beta-based GRM is $grm_{ij} = 2 * (beta_{ij} - beta_{min}) / (1 - beta_{min})$ for $i!=j$, | ^ checkRd: (-1) snpgdsGRM.Rd:66: Lost braces; missing escapes or markup? 66 | beta-based GRM is $grm_{ij} = 2 * (beta_{ij} - beta_{min}) / (1 - beta_{min})$ for $i!=j$, | ^ checkRd: (-1) snpgdsGRM.Rd:66: Lost braces; missing escapes or markup? 66 | beta-based GRM is $grm_{ij} = 2 * (beta_{ij} - beta_{min}) / (1 - beta_{min})$ for $i!=j$, | ^ checkRd: (-1) snpgdsGRM.Rd:67: Lost braces; missing escapes or markup? 67 | $grm_{ij} = 1 + (beta_{i} - beta_{min}) / (1 - beta_{min})$ for $i=j$. It is relative to | ^ checkRd: (-1) snpgdsGRM.Rd:67: Lost braces; missing escapes or markup? 67 | $grm_{ij} = 1 + (beta_{i} - beta_{min}) / (1 - beta_{min})$ for $i=j$. It is relative to | ^ checkRd: (-1) snpgdsGRM.Rd:67: Lost braces; missing escapes or markup? 67 | $grm_{ij} = 1 + (beta_{i} - beta_{min}) / (1 - beta_{min})$ for $i=j$. It is relative to | ^ checkRd: (-1) snpgdsGRM.Rd:67: Lost braces; missing escapes or markup? 67 | $grm_{ij} = 1 + (beta_{i} - beta_{min}) / (1 - beta_{min})$ for $i=j$. It is relative to | ^ * 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 LazyData ... 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed snpgdsMergeGRM 10.533 0.032 10.584 snpgdsGRM 6.964 0.024 6.996 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/00check.log’ for details.
SNPRelate.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SNPRelate ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘SNPRelate’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ConvToGDS.cpp -o ConvToGDS.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_SNPRelate.c -o R_SNPRelate.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SNPRelate.cpp -o SNPRelate.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ThreadPool.cpp -o ThreadPool.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c dGenGWAS.cpp -o dGenGWAS.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c dVect.cpp -o dVect.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genBeta.cpp -o genBeta.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genEIGMIX.cpp -o genEIGMIX.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genFst.cpp -o genFst.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genHWE.cpp -o genHWE.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genIBD.cpp -o genIBD.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genIBS.cpp -o genIBS.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genKING.cpp -o genKING.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genLD.cpp -o genLD.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genPCA.cpp -o genPCA.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/biocbuild/R/R-4.4.1/site-library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c genSlideWin.cpp -o genSlideWin.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o SNPRelate.so 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 -lpthread -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-SNPRelate/00new/SNPRelate/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SNPRelate)
SNPRelate.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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") 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: Wed Aug 21 09:24:19 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Saving to the GDS file: [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:24:22 2024 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: Wed Aug 21 09:24:22 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 4s Saving to the GDS file: [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:24:26 2024 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: Wed Aug 21 09:24:26 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Saving to the GDS file: [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:24:29 2024 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: Wed Aug 21 09:24:29 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Wed Aug 21 09:24:32 2024 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: Wed Aug 21 09:24:32 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s Saving to the GDS file: [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:24:33 2024 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: Wed Aug 21 09:24:33 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Saving to the GDS file: [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s Wed Aug 21 09:24:34 2024 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: Wed Aug 21 09:24:34 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Saving to the GDS file: [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:24:34 2024 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, 1s 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: Wed Aug 21 09:24:35 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:24:35 2024 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: '/home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/plinkhapmap.bed.gz' SNP-major mode (Sample X SNP), 45.7K FAM file: '/home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/plinkhapmap.fam.gz' BIM file: '/home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/plinkhapmap.bim.gz' Wed Aug 21 09:25:27 2024 (store sample id, snp id, position, and chromosome) start writing: 60 samples, 5000 SNPs ... [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:25:27 2024 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: Wed Aug 21 09:25:27 2024 (internal increment: 68676) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s Wed Aug 21 09:25:28 2024 Begin (eigenvalues and eigenvectors) Wed Aug 21 09:25:28 2024 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 Aug 21 09:25:28 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s Wed Aug 21 09:25:29 2024 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 Aug 21 09:25:29 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s Wed Aug 21 09:25:30 2024 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: Wed Aug 21 09:25:30 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 4s Wed Aug 21 09:25:34 2024 Begin (eigenvalues and eigenvectors) Wed Aug 21 09:25:34 2024 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: Wed Aug 21 09:25:34 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Wed Aug 21 09:25:37 2024 Begin (eigenvalues and eigenvectors) Wed Aug 21 09:25:37 2024 Done. FUNCTION: snpgdsAlleleSwitch Strand-switching at 50 SNP locus/loci. Unable to determine switching at 10 SNP locus/loci. FUNCTION: snpgdsApartSelection Wed Aug 21 09:25:37 2024 Chromosome 1, # of SNPs: 367 Wed Aug 21 09:25:38 2024 Chromosome 2, # of SNPs: 367 Wed Aug 21 09:25:38 2024 Chromosome 3, # of SNPs: 317 Wed Aug 21 09:25:38 2024 Chromosome 4, # of SNPs: 295 Wed Aug 21 09:25:38 2024 Chromosome 5, # of SNPs: 295 Wed Aug 21 09:25:38 2024 Chromosome 6, # of SNPs: 283 Wed Aug 21 09:25:38 2024 Chromosome 7, # of SNPs: 245 Wed Aug 21 09:25:38 2024 Chromosome 8, # of SNPs: 234 Wed Aug 21 09:25:38 2024 Chromosome 9, # of SNPs: 202 Wed Aug 21 09:25:38 2024 Chromosome 10, # of SNPs: 224 Wed Aug 21 09:25:38 2024 Chromosome 11, # of SNPs: 223 Wed Aug 21 09:25:38 2024 Chromosome 12, # of SNPs: 208 Wed Aug 21 09:25:38 2024 Chromosome 13, # of SNPs: 172 Wed Aug 21 09:25:38 2024 Chromosome 14, # of SNPs: 147 Wed Aug 21 09:25:38 2024 Chromosome 15, # of SNPs: 121 Wed Aug 21 09:25:38 2024 Chromosome 16, # of SNPs: 129 Wed Aug 21 09:25:38 2024 Chromosome 17, # of SNPs: 116 Wed Aug 21 09:25:38 2024 Chromosome 18, # of SNPs: 129 Wed Aug 21 09:25:38 2024 Chromosome 19, # of SNPs: 73 Wed Aug 21 09:25:38 2024 Chromosome 20, # of SNPs: 106 Wed Aug 21 09:25:38 2024 Chromosome 21, # of SNPs: 62 Wed Aug 21 09:25:38 2024 Chromosome 22, # of SNPs: 51 Wed Aug 21 09:25:38 2024 Chromosome 23, # of SNPs: 204 Total # of SNPs selected:4570 FUNCTION: snpgdsBED2GDS Start file conversion from PLINK BED to SNP GDS ... BED file: '/home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/plinkhapmap.bed.gz' SNP-major mode (Sample X SNP), 45.7K FAM file: '/home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/plinkhapmap.fam.gz' BIM file: '/home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/plinkhapmap.bim.gz' Wed Aug 21 09:25:38 2024 (store sample id, snp id, position, and chromosome) start writing: 60 samples, 5000 SNPs ... [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:25:38 2024 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: Wed Aug 21 09:25:38 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Wed Aug 21 09:25:41 2024 Begin (eigenvalues and eigenvectors) Wed Aug 21 09:25:41 2024 Done. FUNCTION: snpgdsCreateGenoSet SNP pruning based on LD: Excluding 365 SNPs on non-autosomes Excluding 139 SNPs (monomorphic: TRUE, MAF: 0.005, missing rate: 0.05) # of samples: 279 # of SNPs: 8,584 using 1 thread sliding window: 500,000 basepairs, Inf SNPs |LD| threshold: 0.2 method: composite Chrom 1: |====================|====================| 74.30%, 532 / 716 (Wed Aug 21 09:25:41 2024) Chrom 2: |====================|====================| 72.24%, 536 / 742 (Wed Aug 21 09:25:41 2024) Chrom 3: |====================|====================| 73.40%, 447 / 609 (Wed Aug 21 09:25:41 2024) Chrom 4: |====================|====================| 72.42%, 407 / 562 (Wed Aug 21 09:25:41 2024) Chrom 5: |====================|====================| 75.80%, 429 / 566 (Wed Aug 21 09:25:41 2024) Chrom 6: |====================|====================| 73.81%, 417 / 565 (Wed Aug 21 09:25:41 2024) Chrom 7: |====================|====================| 75.21%, 355 / 472 (Wed Aug 21 09:25:41 2024) Chrom 8: |====================|====================| 69.67%, 340 / 488 (Wed Aug 21 09:25:41 2024) Chrom 9: |====================|====================| 76.92%, 320 / 416 (Wed Aug 21 09:25:41 2024) Chrom 10: |====================|====================| 73.08%, 353 / 483 (Wed Aug 21 09:25:41 2024) Chrom 11: |====================|====================| 76.51%, 342 / 447 (Wed Aug 21 09:25:41 2024) Chrom 12: |====================|====================| 74.71%, 319 / 427 (Wed Aug 21 09:25:41 2024) Chrom 13: |====================|====================| 76.74%, 264 / 344 (Wed Aug 21 09:25:41 2024) Chrom 14: |====================|====================| 76.24%, 215 / 282 (Wed Aug 21 09:25:41 2024) Chrom 15: |====================|====================| 75.95%, 199 / 262 (Wed Aug 21 09:25:41 2024) Chrom 16: |====================|====================| 70.86%, 197 / 278 (Wed Aug 21 09:25:41 2024) Chrom 17: |====================|====================| 76.33%, 158 / 207 (Wed Aug 21 09:25:41 2024) Chrom 18: |====================|====================| 73.31%, 195 / 266 (Wed Aug 21 09:25:41 2024) Chrom 19: |====================|====================| 82.50%, 99 / 120 (Wed Aug 21 09:25:41 2024) Chrom 20: |====================|====================| 70.31%, 161 / 229 (Wed Aug 21 09:25:41 2024) Chrom 21: |====================|====================| 75.40%, 95 / 126 (Wed Aug 21 09:25:41 2024) Chrom 22: |====================|====================| 75.86%, 88 / 116 (Wed Aug 21 09:25:41 2024) 6,468 markers are selected in total. Create a GDS genotype file: The new dataset consists of 279 samples and 6468 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 Aug 21 09:25:42 2024 0% Dissimilarity: Wed Aug 21 09:25:43 2024 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 Aug 21 09:25:45 2024 0% Dissimilarity: Wed Aug 21 09:25:47 2024 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 Aug 21 09:25:47 2024 0% Dissimilarity: Wed Aug 21 09:25:49 2024 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: Wed Aug 21 09:25:50 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Wed Aug 21 09:25:53 2024 Begin (eigenvalues and eigenvectors) Wed Aug 21 09:25:53 2024 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 Aug 21 09:25:54 2024 0% Wed Aug 21 09:25:54 2024 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 Aug 21 09:25:54 2024 0% Output: Wed Aug 21 09:25:54 2024 100% Done. FUNCTION: snpgdsGDS2PED Converting from GDS to PLINK PED: Output a MAP file DONE. Output a PED file ... Output: Wed Aug 21 09:25:54 2024 0% Output: Wed Aug 21 09:25:54 2024 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: Wed Aug 21 09:25:54 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 4s Wed Aug 21 09:25:58 2024 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: Wed Aug 21 09:25:58 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 4s Saving to the GDS file: [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:02 2024 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 Aug 21 09:26:03 2024 0% Dissimilarity: Wed Aug 21 09:26:04 2024 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: Wed Aug 21 09:26:05 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:05 2024 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: Wed Aug 21 09:26:06 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:06 2024 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: Wed Aug 21 09:26:07 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:07 2024 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 Aug 21 09:26:07 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:07 2024 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 Aug 21 09:26:07 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s Wed Aug 21 09:26:08 2024 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 Chrom 1: |====================|====================| 54.75%, 392 / 716 (Wed Aug 21 09:26:08 2024) Chrom 2: |====================|====================| 54.85%, 407 / 742 (Wed Aug 21 09:26:08 2024) Chrom 3: |====================|====================| 55.99%, 341 / 609 (Wed Aug 21 09:26:08 2024) Chrom 4: |====================|====================| 56.58%, 318 / 562 (Wed Aug 21 09:26:08 2024) Chrom 5: |====================|====================| 56.36%, 319 / 566 (Wed Aug 21 09:26:08 2024) Chrom 6: |====================|====================| 53.45%, 302 / 565 (Wed Aug 21 09:26:08 2024) Chrom 7: |====================|====================| 55.72%, 263 / 472 (Wed Aug 21 09:26:08 2024) Chrom 8: |====================|====================| 50.82%, 248 / 488 (Wed Aug 21 09:26:08 2024) Chrom 9: |====================|====================| 54.81%, 228 / 416 (Wed Aug 21 09:26:08 2024) Chrom 10: |====================|====================| 49.90%, 241 / 483 (Wed Aug 21 09:26:08 2024) Chrom 11: |====================|====================| 54.81%, 245 / 447 (Wed Aug 21 09:26:08 2024) Chrom 12: |====================|====================| 54.57%, 233 / 427 (Wed Aug 21 09:26:08 2024) Chrom 13: |====================|====================| 53.49%, 184 / 344 (Wed Aug 21 09:26:08 2024) Chrom 14: |====================|====================| 56.03%, 158 / 282 (Wed Aug 21 09:26:08 2024) Chrom 15: |====================|====================| 54.58%, 143 / 262 (Wed Aug 21 09:26:08 2024) Chrom 16: |====================|====================| 54.68%, 152 / 278 (Wed Aug 21 09:26:08 2024) Chrom 17: |====================|====================| 55.56%, 115 / 207 (Wed Aug 21 09:26:08 2024) Chrom 18: |====================|====================| 55.64%, 148 / 266 (Wed Aug 21 09:26:08 2024) Chrom 19: |====================|====================| 66.67%, 80 / 120 (Wed Aug 21 09:26:08 2024) Chrom 20: |====================|====================| 53.28%, 122 / 229 (Wed Aug 21 09:26:08 2024) Chrom 21: |====================|====================| 50.79%, 64 / 126 (Wed Aug 21 09:26:08 2024) Chrom 22: |====================|====================| 51.72%, 60 / 116 (Wed Aug 21 09:26:08 2024) 4,763 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) = 8025 MLE IBD: Wed Aug 21 09:26:08 2024 0% MLE IBD: Wed Aug 21 09:26:08 2024 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: 0.536, sd: 0.286 MLE IBD: the sum of all selected genotypes (0,1,2) = 6690 MLE IBD: Wed Aug 21 09:26:08 2024 0% MLE IBD: Wed Aug 21 09:26:09 2024 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 Chrom 1: |====================|====================| 54.75%, 392 / 716 (Wed Aug 21 09:26:09 2024) Chrom 2: |====================|====================| 54.85%, 407 / 742 (Wed Aug 21 09:26:09 2024) Chrom 3: |====================|====================| 55.99%, 341 / 609 (Wed Aug 21 09:26:09 2024) Chrom 4: |====================|====================| 56.58%, 318 / 562 (Wed Aug 21 09:26:09 2024) Chrom 5: |====================|====================| 56.36%, 319 / 566 (Wed Aug 21 09:26:09 2024) Chrom 6: |====================|====================| 53.45%, 302 / 565 (Wed Aug 21 09:26:09 2024) Chrom 7: |====================|====================| 55.72%, 263 / 472 (Wed Aug 21 09:26:09 2024) Chrom 8: |====================|====================| 50.82%, 248 / 488 (Wed Aug 21 09:26:09 2024) Chrom 9: |====================|====================| 54.81%, 228 / 416 (Wed Aug 21 09:26:09 2024) Chrom 10: |====================|====================| 49.90%, 241 / 483 (Wed Aug 21 09:26:09 2024) Chrom 11: |====================|====================| 54.81%, 245 / 447 (Wed Aug 21 09:26:09 2024) Chrom 12: |====================|====================| 54.57%, 233 / 427 (Wed Aug 21 09:26:09 2024) Chrom 13: |====================|====================| 53.49%, 184 / 344 (Wed Aug 21 09:26:09 2024) Chrom 14: |====================|====================| 56.03%, 158 / 282 (Wed Aug 21 09:26:09 2024) Chrom 15: |====================|====================| 54.58%, 143 / 262 (Wed Aug 21 09:26:09 2024) Chrom 16: |====================|====================| 54.68%, 152 / 278 (Wed Aug 21 09:26:09 2024) Chrom 17: |====================|====================| 55.56%, 115 / 207 (Wed Aug 21 09:26:09 2024) Chrom 18: |====================|====================| 55.64%, 148 / 266 (Wed Aug 21 09:26:09 2024) Chrom 19: |====================|====================| 66.67%, 80 / 120 (Wed Aug 21 09:26:09 2024) Chrom 20: |====================|====================| 53.28%, 122 / 229 (Wed Aug 21 09:26:09 2024) Chrom 21: |====================|====================| 50.79%, 64 / 126 (Wed Aug 21 09:26:09 2024) Chrom 22: |====================|====================| 51.72%, 60 / 116 (Wed Aug 21 09:26:09 2024) 4,763 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) = 8025 MLE IBD: Wed Aug 21 09:26:09 2024 0% MLE IBD: Wed Aug 21 09:26:09 2024 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: 0.536, sd: 0.286 MLE IBD: the sum of all selected genotypes (0,1,2) = 6690 MLE IBD: Wed Aug 21 09:26:09 2024 0% MLE IBD: Wed Aug 21 09:26:09 2024 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 Aug 21 09:26:09 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:09 2024 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 Aug 21 09:26:09 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:09 2024 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 Aug 21 09:26:10 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:10 2024 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 Aug 21 09:26:10 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:10 2024 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 Aug 21 09:26:10 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:10 2024 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 Aug 21 09:26:10 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:10 2024 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 Aug 21 09:26:10 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s Wed Aug 21 09:26:11 2024 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: Wed Aug 21 09:26:11 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:11 2024 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 139 SNPs (monomorphic: TRUE, MAF: 0.005, missing rate: 0.05) # of samples: 279 # of SNPs: 8,584 using 1 thread sliding window: 500,000 basepairs, Inf SNPs |LD| threshold: 0.2 method: composite Chrom 1: |====================|====================| 74.30%, 532 / 716 (Wed Aug 21 09:26:12 2024) Chrom 2: |====================|====================| 72.24%, 536 / 742 (Wed Aug 21 09:26:12 2024) Chrom 3: |====================|====================| 73.40%, 447 / 609 (Wed Aug 21 09:26:12 2024) Chrom 4: |====================|====================| 72.42%, 407 / 562 (Wed Aug 21 09:26:12 2024) Chrom 5: |====================|====================| 75.80%, 429 / 566 (Wed Aug 21 09:26:12 2024) Chrom 6: |====================|====================| 73.81%, 417 / 565 (Wed Aug 21 09:26:12 2024) Chrom 7: |====================|====================| 75.21%, 355 / 472 (Wed Aug 21 09:26:12 2024) Chrom 8: |====================|====================| 69.67%, 340 / 488 (Wed Aug 21 09:26:12 2024) Chrom 9: |====================|====================| 76.92%, 320 / 416 (Wed Aug 21 09:26:12 2024) Chrom 10: |====================|====================| 73.08%, 353 / 483 (Wed Aug 21 09:26:12 2024) Chrom 11: |====================|====================| 76.51%, 342 / 447 (Wed Aug 21 09:26:12 2024) Chrom 12: |====================|====================| 74.71%, 319 / 427 (Wed Aug 21 09:26:12 2024) Chrom 13: |====================|====================| 76.74%, 264 / 344 (Wed Aug 21 09:26:12 2024) Chrom 14: |====================|====================| 76.24%, 215 / 282 (Wed Aug 21 09:26:12 2024) Chrom 15: |====================|====================| 75.95%, 199 / 262 (Wed Aug 21 09:26:12 2024) Chrom 16: |====================|====================| 70.86%, 197 / 278 (Wed Aug 21 09:26:12 2024) Chrom 17: |====================|====================| 76.33%, 158 / 207 (Wed Aug 21 09:26:12 2024) Chrom 18: |====================|====================| 73.31%, 195 / 266 (Wed Aug 21 09:26:12 2024) Chrom 19: |====================|====================| 82.50%, 99 / 120 (Wed Aug 21 09:26:12 2024) Chrom 20: |====================|====================| 70.31%, 161 / 229 (Wed Aug 21 09:26:12 2024) Chrom 21: |====================|====================| 75.40%, 95 / 126 (Wed Aug 21 09:26:12 2024) Chrom 22: |====================|====================| 75.86%, 88 / 116 (Wed Aug 21 09:26:12 2024) 6,468 markers are selected in total. List of 22 $ chr1 : int [1:532] 1 2 4 5 7 10 12 14 15 16 ... $ chr2 : int [1:536] 717 718 719 720 721 723 724 725 726 727 ... $ chr3 : int [1:447] 1459 1461 1464 1466 1468 1469 1471 1472 1473 1476 ... $ chr4 : int [1:407] 2068 2069 2070 2071 2072 2074 2075 2076 2077 2078 ... $ chr5 : int [1:429] 2630 2631 2635 2636 2637 2638 2640 2642 2643 2645 ... $ chr6 : int [1:417] 3196 3197 3198 3200 3201 3204 3205 3206 3207 3208 ... $ chr7 : int [1:355] 3761 3762 3763 3766 3767 3768 3770 3771 3772 3773 ... $ chr8 : int [1:340] 4233 4234 4235 4236 4237 4238 4239 4240 4241 4242 ... $ chr9 : int [1:320] 4721 4722 4724 4727 4728 4730 4731 4732 4733 4735 ... $ chr10: int [1:353] 5138 5139 5140 5143 5144 5145 5146 5147 5148 5149 ... $ chr11: int [1:342] 5620 5623 5624 5625 5626 5628 5629 5630 5631 5632 ... $ chr12: int [1:319] 6067 6068 6069 6070 6073 6074 6075 6077 6078 6079 ... $ chr13: int [1:264] 6494 6497 6498 6499 6500 6501 6503 6505 6507 6509 ... $ chr14: int [1:215] 6840 6841 6842 6843 6844 6845 6846 6847 6848 6850 ... $ chr15: int [1:199] 7120 7121 7122 7124 7125 7126 7127 7128 7129 7130 ... $ chr16: int [1:197] 7382 7383 7384 7385 7387 7388 7389 7391 7392 7394 ... $ chr17: int [1:158] 7660 7661 7662 7663 7664 7665 7666 7667 7668 7669 ... $ chr18: int [1:195] 7867 7868 7869 7870 7871 7872 7873 7874 7875 7877 ... $ chr19: int [1:99] 8133 8135 8136 8137 8138 8139 8140 8141 8142 8144 ... $ chr20: int [1:161] 8253 8254 8257 8258 8259 8260 8261 8262 8265 8266 ... $ chr21: int [1:95] 8482 8484 8485 8486 8487 8488 8489 8490 8491 8492 ... $ chr22: int [1:88] 8608 8609 8610 8612 8613 8614 8615 8617 8618 8620 ... 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: Wed Aug 21 09:26:12 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 4s Wed Aug 21 09:26:16 2024 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: Wed Aug 21 09:26:16 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Saving to the GDS file: [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:19 2024 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: Wed Aug 21 09:26:19 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Saving to the GDS file: [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 1s Wed Aug 21 09:26:23 2024 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: Wed Aug 21 09:26:23 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Wed Aug 21 09:26:26 2024 Begin (eigenvalues and eigenvectors) Wed Aug 21 09:26:26 2024 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: Wed Aug 21 09:26:26 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 4s Wed Aug 21 09:26:30 2024 Begin (eigenvalues and eigenvectors) Wed Aug 21 09:26:30 2024 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 Aug 21 09:26:30 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:30 2024 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 Aug 21 09:26:30 2024 [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:30 2024 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: Wed Aug 21 09:26:30 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Wed Aug 21 09:26:33 2024 Begin (eigenvalues and eigenvectors) Wed Aug 21 09:26:33 2024 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 Aug 21 09:26:33 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:33 2024 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: Wed Aug 21 09:26:33 2024 (internal increment: 14768) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 3s Wed Aug 21 09:26:36 2024 Begin (eigenvalues and eigenvectors) Wed Aug 21 09:26:36 2024 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 Aug 21 09:26:36 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:36 2024 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 Aug 21 09:26:36 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:36 2024 Done. FUNCTION: snpgdsPED2GDS Converting from GDS to PLINK PED: Output a MAP file DONE. Output a PED file ... Output: Wed Aug 21 09:26:36 2024 0% Output: Wed Aug 21 09:26:37 2024 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 Chrom 1: |====================|====================| 62.29%, 446 / 716 (Wed Aug 21 09:26:38 2024) Chrom 2: |====================|====================| 62.26%, 462 / 742 (Wed Aug 21 09:26:38 2024) Chrom 3: |====================|====================| 60.10%, 366 / 609 (Wed Aug 21 09:26:38 2024) Chrom 4: |====================|====================| 64.41%, 362 / 562 (Wed Aug 21 09:26:38 2024) Chrom 5: |====================|====================| 62.90%, 356 / 566 (Wed Aug 21 09:26:38 2024) Chrom 6: |====================|====================| 60.18%, 340 / 565 (Wed Aug 21 09:26:38 2024) Chrom 7: |====================|====================| 63.14%, 298 / 472 (Wed Aug 21 09:26:38 2024) Chrom 8: |====================|====================| 57.58%, 281 / 488 (Wed Aug 21 09:26:38 2024) Chrom 9: |====================|====================| 62.98%, 262 / 416 (Wed Aug 21 09:26:38 2024) Chrom 10: |====================|====================| 60.46%, 292 / 483 (Wed Aug 21 09:26:38 2024) Chrom 11: |====================|====================| 63.09%, 282 / 447 (Wed Aug 21 09:26:38 2024) Chrom 12: |====================|====================| 62.76%, 268 / 427 (Wed Aug 21 09:26:38 2024) Chrom 13: |====================|====================| 63.08%, 217 / 344 (Wed Aug 21 09:26:38 2024) Chrom 14: |====================|====================| 63.83%, 180 / 282 (Wed Aug 21 09:26:38 2024) Chrom 15: |====================|====================| 63.74%, 167 / 262 (Wed Aug 21 09:26:38 2024) Chrom 16: |====================|====================| 62.23%, 173 / 278 (Wed Aug 21 09:26:38 2024) Chrom 17: |====================|====================| 65.70%, 136 / 207 (Wed Aug 21 09:26:38 2024) Chrom 18: |====================|====================| 59.40%, 158 / 266 (Wed Aug 21 09:26:38 2024) Chrom 19: |====================|====================| 68.33%, 82 / 120 (Wed Aug 21 09:26:38 2024) Chrom 20: |====================|====================| 66.38%, 152 / 229 (Wed Aug 21 09:26:38 2024) Chrom 21: |====================|====================| 61.11%, 77 / 126 (Wed Aug 21 09:26:38 2024) Chrom 22: |====================|====================| 57.76%, 67 / 116 (Wed Aug 21 09:26:38 2024) 5,424 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: 0.508, sd: 0.281 MLE IBD: the sum of all selected genotypes (0,1,2) = 6317 MLE IBD: Wed Aug 21 09:26:38 2024 0% MLE IBD: Wed Aug 21 09:26:38 2024 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: 0.508, sd: 0.281 *** 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) = 6317 Wed Aug 21 09:26:38 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:38 2024 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: 0.508, sd: 0.281 MLE IBD: the sum of all selected genotypes (0,1,2) = 6317 MLE IBD: Wed Aug 21 09:26:38 2024 0% MLE IBD: Wed Aug 21 09:26:39 2024 100% Genotype matrix: 250 SNPs X 25 samples [1] -384.5064 [1] -379.8635 [1] -389.2882 [1] -390.0637 [1] -405.3267 [1] -386.6771 [1] -382.3052 [1] -375.7884 [1] -400.5859 [1] -379.9675 [1] -372.4947 [1] -372.3346 [1] -393.543 [1] -387.7755 [1] -373.858 [1] -380.4349 [1] -389.0108 [1] -402.2013 [1] -393.1451 [1] -388.5999 [1] -383.8134 [1] -376.6837 [1] -385.4354 [1] -378.9947 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 Chrom 1: |====================|====================| 62.29%, 446 / 716 (Wed Aug 21 09:26:39 2024) Chrom 2: |====================|====================| 62.26%, 462 / 742 (Wed Aug 21 09:26:39 2024) Chrom 3: |====================|====================| 60.10%, 366 / 609 (Wed Aug 21 09:26:39 2024) Chrom 4: |====================|====================| 64.41%, 362 / 562 (Wed Aug 21 09:26:39 2024) Chrom 5: |====================|====================| 62.90%, 356 / 566 (Wed Aug 21 09:26:39 2024) Chrom 6: |====================|====================| 60.18%, 340 / 565 (Wed Aug 21 09:26:39 2024) Chrom 7: |====================|====================| 63.14%, 298 / 472 (Wed Aug 21 09:26:39 2024) Chrom 8: |====================|====================| 57.58%, 281 / 488 (Wed Aug 21 09:26:39 2024) Chrom 9: |====================|====================| 62.98%, 262 / 416 (Wed Aug 21 09:26:39 2024) Chrom 10: |====================|====================| 60.46%, 292 / 483 (Wed Aug 21 09:26:39 2024) Chrom 11: |====================|====================| 63.09%, 282 / 447 (Wed Aug 21 09:26:39 2024) Chrom 12: |====================|====================| 62.76%, 268 / 427 (Wed Aug 21 09:26:39 2024) Chrom 13: |====================|====================| 63.08%, 217 / 344 (Wed Aug 21 09:26:39 2024) Chrom 14: |====================|====================| 63.83%, 180 / 282 (Wed Aug 21 09:26:39 2024) Chrom 15: |====================|====================| 63.74%, 167 / 262 (Wed Aug 21 09:26:39 2024) Chrom 16: |====================|====================| 62.23%, 173 / 278 (Wed Aug 21 09:26:39 2024) Chrom 17: |====================|====================| 65.70%, 136 / 207 (Wed Aug 21 09:26:39 2024) Chrom 18: |====================|====================| 59.40%, 158 / 266 (Wed Aug 21 09:26:39 2024) Chrom 19: |====================|====================| 68.33%, 82 / 120 (Wed Aug 21 09:26:39 2024) Chrom 20: |====================|====================| 66.38%, 152 / 229 (Wed Aug 21 09:26:39 2024) Chrom 21: |====================|====================| 61.11%, 77 / 126 (Wed Aug 21 09:26:39 2024) Chrom 22: |====================|====================| 57.76%, 67 / 116 (Wed Aug 21 09:26:39 2024) 5,424 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: 0.508, sd: 0.281 MLE IBD: the sum of all selected genotypes (0,1,2) = 6317 MLE IBD: Wed Aug 21 09:26:39 2024 0% MLE IBD: Wed Aug 21 09:26:40 2024 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: 0.508, sd: 0.281 *** 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) = 6317 Wed Aug 21 09:26:40 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:40 2024 Done. Genotype matrix: 250 SNPs X 25 samples [1] -384.5064 [1] -379.8635 [1] -389.2882 [1] -390.0637 [1] -405.3267 [1] -386.6771 [1] -382.3052 [1] -375.7884 [1] -400.5859 [1] -379.9675 [1] -372.4947 [1] -372.3346 [1] -393.543 [1] -387.7755 [1] -373.858 [1] -380.4349 [1] -389.0108 [1] -402.2013 [1] -393.1451 [1] -388.5999 [1] -383.8134 [1] -376.6837 [1] -385.4354 [1] -378.9947 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: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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 Aug 21 09:26:40 2024, Chromosome 1 (716 SNPs), 2448 windows Wed Aug 21 09:26:40 2024, Chromosome 2 (742 SNPs), 2416 windows Wed Aug 21 09:26:41 2024, Chromosome 3 (609 SNPs), 1985 windows Wed Aug 21 09:26:41 2024, Chromosome 4 (562 SNPs), 1894 windows Wed Aug 21 09:26:41 2024, Chromosome 5 (566 SNPs), 1797 windows Wed Aug 21 09:26:41 2024, Chromosome 6 (565 SNPs), 1694 windows Wed Aug 21 09:26:41 2024, Chromosome 7 (472 SNPs), 1573 windows Wed Aug 21 09:26:41 2024, Chromosome 8 (488 SNPs), 1445 windows Wed Aug 21 09:26:41 2024, Chromosome 9 (416 SNPs), 1393 windows Wed Aug 21 09:26:41 2024, Chromosome 10 (483 SNPs), 1343 windows Wed Aug 21 09:26:41 2024, Chromosome 11 (447 SNPs), 1338 windows Wed Aug 21 09:26:41 2024, Chromosome 12 (427 SNPs), 1316 windows Wed Aug 21 09:26:41 2024, Chromosome 13 (344 SNPs), 948 windows Wed Aug 21 09:26:41 2024, Chromosome 14 (281 SNPs), 847 windows Wed Aug 21 09:26:41 2024, Chromosome 15 (262 SNPs), 774 windows Wed Aug 21 09:26:41 2024, Chromosome 16 (278 SNPs), 873 windows Wed Aug 21 09:26:41 2024, Chromosome 17 (207 SNPs), 773 windows Wed Aug 21 09:26:41 2024, Chromosome 18 (266 SNPs), 753 windows Wed Aug 21 09:26:41 2024, Chromosome 19 (120 SNPs), 627 windows Wed Aug 21 09:26:41 2024, Chromosome 20 (229 SNPs), 602 windows Wed Aug 21 09:26:41 2024, Chromosome 21 (126 SNPs), 311 windows Wed Aug 21 09:26:41 2024, Chromosome 22 (116 SNPs), 312 windows Wed Aug 21 09:26:41 2024, Chromosome 23 (358 SNPs), 1507 windows Wed Aug 21 09:26:41 2024 Done. FUNCTION: snpgdsSummary The file name: /home/biocbuild/R/R-4.4.1/site-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: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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 "/home/biocbuild/R/R-4.4.1/site-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: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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 "/home/biocbuild/R/R-4.4.1/site-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: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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 "/home/biocbuild/R/R-4.4.1/site-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: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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 "/home/biocbuild/R/R-4.4.1/site-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: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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 "/home/biocbuild/R/R-4.4.1/site-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: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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: /home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/sequence.vcf content: 5 rows x 12 columns Wed Aug 21 09:26:42 2024 store sample id, snp id, position, and chromosome. start writing: 3 samples, 2 SNPs ... file: /home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/sequence.vcf [1] 1 Wed Aug 21 09:26:42 2024 Done. The file name: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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: /home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/sequence.vcf content: 5 rows x 12 columns Wed Aug 21 09:26:42 2024 store sample id, snp id, position, and chromosome. start writing: 3 samples, 2 SNPs ... file: /home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/sequence.vcf [1] 1 Wed Aug 21 09:26:42 2024 Done. The file name: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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: /home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/sequence.vcf content: 5 rows x 12 columns Wed Aug 21 09:26:42 2024 store sample id, snp id, position, and chromosome. start writing: 3 samples, 5 SNPs ... file: /home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/sequence.vcf Wed Aug 21 09:26:42 2024 Done. Some of 'snp.allele' are not standard (e.g., A/G,T). The file name: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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: /home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/sequence.vcf content: 5 rows x 12 columns Wed Aug 21 09:26:42 2024 store sample id, snp id, position, and chromosome. start writing: 3 samples, 5 SNPs ... file: /home/biocbuild/R/R-4.4.1/site-library/SNPRelate/extdata/sequence.vcf Wed Aug 21 09:26:42 2024 Done. Some of 'snp.allele' are not standard (e.g., A/G,T). The file name: /home/biocbuild/bbs-3.20-bioc/meat/SNPRelate.Rcheck/tests/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 Aug 21 09:26:46 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:46 2024 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 Aug 21 09:26:46 2024 [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:46 2024 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 Aug 21 09:26:46 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:46 2024 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 Aug 21 09:26:46 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:46 2024 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 Aug 21 09:26:47 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:47 2024 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 Aug 21 09:26:47 2024 [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:47 2024 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 Aug 21 09:26:47 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:47 2024 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 Aug 21 09:26:47 2024 (internal increment: 65536) [..................................................] 0%, ETC: --- [==================================================] 100%, completed, 0s Wed Aug 21 09:26:47 2024 Done. RUNIT TEST PROTOCOL -- Wed Aug 21 09:26:47 2024 *********************************************** 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 148.787 1.376 149.350
SNPRelate.Rcheck/SNPRelate-Ex.timings
name | user | system | elapsed | |
SNPGDSFileClass-class | 0.003 | 0.008 | 0.010 | |
SNPRelate-package | 2.543 | 0.052 | 2.607 | |
snpgdsAdmixPlot | 3.744 | 0.004 | 3.754 | |
snpgdsAdmixProp | 3.406 | 0.032 | 3.443 | |
snpgdsAlleleSwitch | 0.078 | 0.000 | 0.079 | |
snpgdsApartSelection | 0.105 | 0.004 | 0.109 | |
snpgdsBED2GDS | 0.114 | 0.008 | 0.123 | |
snpgdsClose | 0.007 | 0.000 | 0.006 | |
snpgdsCombineGeno | 0.102 | 0.004 | 0.107 | |
snpgdsCreateGeno | 3.517 | 0.012 | 3.534 | |
snpgdsCreateGenoSet | 0.119 | 0.004 | 0.136 | |
snpgdsCutTree | 3.215 | 0.072 | 3.292 | |
snpgdsDiss | 2.828 | 0.004 | 2.835 | |
snpgdsDrawTree | 2.611 | 0.004 | 2.616 | |
snpgdsEIGMIX | 3.300 | 0.000 | 3.305 | |
snpgdsErrMsg | 0 | 0 | 0 | |
snpgdsExampleFileName | 0.001 | 0.000 | 0.001 | |
snpgdsFst | 0.040 | 0.004 | 0.044 | |
snpgdsGDS2BED | 0.047 | 0.008 | 0.055 | |
snpgdsGDS2Eigen | 0.146 | 0.012 | 0.159 | |
snpgdsGDS2PED | 0.359 | 0.024 | 0.384 | |
snpgdsGEN2GDS | 0 | 0 | 0 | |
snpgdsGRM | 6.964 | 0.024 | 6.996 | |
snpgdsGetGeno | 0.088 | 0.000 | 0.089 | |
snpgdsHCluster | 2.819 | 0.008 | 2.830 | |
snpgdsHWE | 0.018 | 0.000 | 0.019 | |
snpgdsIBDKING | 2.150 | 0.020 | 2.174 | |
snpgdsIBDMLE | 0.728 | 0.008 | 0.737 | |
snpgdsIBDMLELogLik | 0.724 | 0.008 | 0.732 | |
snpgdsIBDMoM | 0.341 | 0.024 | 0.365 | |
snpgdsIBDSelection | 0.129 | 0.004 | 0.133 | |
snpgdsIBS | 0.495 | 0.008 | 0.503 | |
snpgdsIBSNum | 0.738 | 0.004 | 0.743 | |
snpgdsIndInb | 0.036 | 0.000 | 0.036 | |
snpgdsIndInbCoef | 0.009 | 0.000 | 0.010 | |
snpgdsIndivBeta | 0.402 | 0.000 | 0.404 | |
snpgdsLDMat | 0.239 | 0.008 | 0.248 | |
snpgdsLDpair | 0.004 | 0.000 | 0.004 | |
snpgdsLDpruning | 0.059 | 0.012 | 0.071 | |
snpgdsMergeGRM | 10.533 | 0.032 | 10.584 | |
snpgdsOpen | 0.007 | 0.000 | 0.007 | |
snpgdsOption | 0.002 | 0.000 | 0.002 | |
snpgdsPCA | 3.605 | 0.016 | 3.628 | |
snpgdsPCACorr | 3.602 | 0.008 | 3.617 | |
snpgdsPCASNPLoading | 3.471 | 0.000 | 3.477 | |
snpgdsPCASampLoading | 3.456 | 0.000 | 3.462 | |
snpgdsPED2GDS | 1.204 | 0.054 | 1.267 | |
snpgdsPairIBD | 1.401 | 0.012 | 1.419 | |
snpgdsPairIBDMLELogLik | 0.562 | 0.010 | 0.572 | |
snpgdsPairScore | 0.218 | 0.078 | 0.297 | |
snpgdsSNPList | 0.011 | 0.000 | 0.011 | |
snpgdsSNPListIntersect | 0.069 | 0.000 | 0.070 | |
snpgdsSNPRateFreq | 0.113 | 0.004 | 0.118 | |
snpgdsSampMissRate | 0.008 | 0.000 | 0.008 | |
snpgdsSelectSNP | 0.009 | 0.000 | 0.009 | |
snpgdsSlidingWindow | 1.110 | 0.004 | 1.117 | |
snpgdsSummary | 0.055 | 0.000 | 0.056 | |
snpgdsTranspose | 0.159 | 0.004 | 0.163 | |
snpgdsVCF2GDS | 0.102 | 0.032 | 0.135 | |
snpgdsVCF2GDS_R | 0.058 | 0.004 | 0.063 | |