Closed richelbilderbeek closed 2 years ago
[richel@sens2021565-bianca ~]$ singularity run nsphs_ml_qt/nsphs_ml_qt.sif /opt/plinkr/plink_1_9_unix/plink --bfile data_issue_5/data_issue_5 --pheno data_issue_5/data_issue_5.phe --allow-no-sex --assoc --out result 'nsphs_ml_qt.sif' running with arguments '/opt/plinkr/plink_1_9_unix/plink --bfile data_issue_5/data_issue_5 --pheno data_issue_5/data_issue_5.phe --allow-no-sex --assoc --out result' PLINK v1.90b6.22 64-bit (16 Apr 2021) www.cog-genomics.org/plink/1.9/ (C) 2005-2021 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to result.log. Options in effect: --allow-no-sex --assoc --bfile data_issue_5/data_issue_5 --out result --pheno data_issue_5/data_issue_5.phe 7317 MB RAM detected; reserving 3658 MB for main workspace. 10 variants loaded from .bim file. 870 people (0 males, 0 females, 870 ambiguous) loaded from .fam. Ambiguous sex IDs written to result.nosex . 870 phenotype values present after --pheno. Using 1 thread. Before main variant filters, 870 founders and 0 nonfounders present. Calculating allele frequencies... done. 10 variants and 870 people pass filters and QC. Phenotype data is quantitative. Writing QT --assoc report to result.qassoc ... done. [richel@sens2021565-bianca ~]$ ls 21_create_issue_5_params.log 29_zip_issue_5.log data_issue_5 nsphs_ml_qt README.md result.qassoc 22_create_issue_5_data.log 98_clean_bianca.sh data_issue_5_ae plink.log result.log richel-sens2021565 25_run_issue_5.log bin GenoCAE plink.nosex result.nosex [richel@sens2021565-bianca ~]$ cat result.qassoc CHR SNP BP NMISS BETA SE R2 T P 1 rs183074751 154452560 870 0.5162 0.149 0.01363 3.463 0.0005594 1 rs7526131 154452659 870 -0.9611 0.03401 0.4792 -28.26 4.216e-125 1 . 154452779 870 0.2791 0.5037 0.0003536 0.5541 0.5797 1 . 154452860 870 -0.7479 0.4501 0.00317 -1.662 0.09697 1 . 154452861 870 -0.7479 0.4501 0.00317 -1.662 0.09697 1 rs12126142 154452980 870 1.239 0.02812 0.691 44.06 1.466e-223 1 . 154453110 870 -0.1942 1.006 4.296e-05 -0.1931 0.8469 1 . 154453121 870 -0.1942 1.006 4.296e-05 -0.1931 0.8469 1 . 154453122 870 -0.1942 1.006 4.296e-05 -0.1931 0.8469 1 . 154453390 870 -0.4463 0.7115 0.0004532 -0.6273 0.5306
Note that although a window of 1kb was used, only 10 variants were there.
But, a good find nonetheless!