plink Error: Failed to extract eigenvector(s) from GRM.
Error: Failed to extract eigenvector(s) from GRM.
001、
root@DESKTOP-1N42TVH:/home/test5# ls test.map test.ped root@DESKTOP-1N42TVH:/home/test5# cat test.map 1 rs11260595 0 1028961 1 rs6671356 0 1029889 1 rs6604968 0 1031563 1 rs4970405 0 1038818 1 rs12726255 0 1039813 1 rs4970409 0 1043315 1 rs7548798 0 1050037 1 rs17160824 0 1050471 1 rs11807848 0 1051029 1 rs12757754 0 1051125 root@DESKTOP-1N42TVH:/home/test5# cat test.ped 1444 NA12739 0 0 1 -9 C C C T G A G A G A A G C C A G C T G A 1344 NA10850 0 k 2 -9 A C C T G A A A G A G G T C G G C T A A 1328 NA06984 0 0 1 2 C C C T G A G A G A A G C C A G C T G A 1463 NA12877 0 0 1 -9 C C T T A A A A A A G G C C G G T T A A 1418 NA12275 0 0 2 1 C C T T A A A A A A G G C C G G T T A A 13291 NA06986 0 0 1 1 C C C T G A G A G A A G C C A G C T G A root@DESKTOP-1N42TVH:/home/test5# plink --file test --pca 3 PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/ (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to plink.log. Options in effect: --file test --pca 3 16007 MB RAM detected; reserving 8003 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (10 variants, 6 people). --file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam written. 10 variants loaded from .bim file. 6 people (4 males, 2 females) loaded from .fam. 3 phenotype values loaded from .fam. Using up to 11 threads (change this with --threads). Before main variant filters, 5 founders and 1 nonfounder present. Calculating allele frequencies... done. Total genotyping rate is exactly 1. 10 variants and 6 people pass filters and QC. Among remaining phenotypes, 1 is a case and 2 are controls. (3 phenotypes are missing.) Relationship matrix calculation complete. [extracting eigenvalues and eigenvectors] Error: Failed to extract eigenvector(s) from GRM.
002、
root@DESKTOP-1N42TVH:/home/test5# ls test.map test.ped root@DESKTOP-1N42TVH:/home/test5# cat test.map 1 rs11260595 0 1028961 1 rs6671356 0 1029889 1 rs6604968 0 1031563 1 rs4970405 0 1038818 1 rs12726255 0 1039813 1 rs4970409 0 1043315 1 rs7548798 0 1050037 1 rs17160824 0 1050471 1 rs11807848 0 1051029 1 rs12757754 0 1051125 root@DESKTOP-1N42TVH:/home/test5# cat test.ped 1444 NA12739 0 0 1 -9 C C C T G A G A G A A G C C A G C T G A 1344 NA10850 0 0 2 -9 A C C T G A A A G A G G T C G G C T A A 1328 NA06984 0 0 1 2 C C C T G A G A G A A G C C A G C T G A 1463 NA12877 0 0 1 -9 C C T T A A A A A A G G C C G G T T A A 1418 NA12275 0 0 2 1 C C T T A A A A A A G G C C G G T T A A 13291 NA06986 0 0 1 1 C C C T G A G A G A A G C C A G C T G A root@DESKTOP-1N42TVH:/home/test5# plink --file test --pca 3 PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/ (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to plink.log. Options in effect: --file test --pca 3 16007 MB RAM detected; reserving 8003 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (10 variants, 6 people). --file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam written. 10 variants loaded from .bim file. 6 people (4 males, 2 females) loaded from .fam. 3 phenotype values loaded from .fam. Using up to 11 threads (change this with --threads). Before main variant filters, 6 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is exactly 1. 10 variants and 6 people pass filters and QC. Among remaining phenotypes, 1 is a case and 2 are controls. (3 phenotypes are missing.) Relationship matrix calculation complete. --pca: Results saved to plink.eigenval and plink.eigenvec .
