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| author | Pjotr Prins | 2022-03-12 14:39:18 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2022-03-12 14:39:18 +0100 |
| commit | 2853fd10c1de29221d87b101e49c0fee7d61f520 (patch) | |
| tree | 0e2b6301c7c0e2150cd2cec5555ae810561d2095 /issues/gemma | |
| parent | 403bb5b1e546944ad561e27562337aef154b5836 (diff) | |
| download | gn-gemtext-2853fd10c1de29221d87b101e49c0fee7d61f520.tar.gz | |
issue: gemma: is decent for running the LMM
Diffstat (limited to 'issues/gemma')
| -rw-r--r-- | issues/gemma/HS-Rat-crashes-gemma.gmi | 25 |
1 files changed, 25 insertions, 0 deletions
diff --git a/issues/gemma/HS-Rat-crashes-gemma.gmi b/issues/gemma/HS-Rat-crashes-gemma.gmi index 6d8f5c8..5d0171a 100644 --- a/issues/gemma/HS-Rat-crashes-gemma.gmi +++ b/issues/gemma/HS-Rat-crashes-gemma.gmi @@ -93,6 +93,31 @@ Next run lmm with ``` /usr/bin/time -v gemma -loco 1 -lmm 9 -g HSNIH-Palmer_true_geno.txt -p PHENO_2+FcfQiTVSC7FmmbsatUPg.txt -a HSNIH-Palmer_true_snps.txt -k output/result.cXX.txt + +GEMMA 0.98.5-pre1 (2021-08-14) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 +Reading Files ... +## number of total individuals = 6147 +## number of analyzed individuals = 1306 +## number of covariates = 1 +## number of phenotypes = 1 +## leave one chromosome out (LOCO) = 1 +## number of total SNPs/var = 134918 +## number of SNPS for K = 121094 +## number of SNPS for GWAS = 13824 +## number of analyzed SNPs = 132628 +Start Eigen-Decomposition... +pve estimate =0.161934 +se(pve) =0.0355033 +================================================== 100% +**** INFO: Done. + Command being timed: "gemma -loco 1 -lmm 9 -g HSNIH-Palmer_true_geno.txt -p PHENO_2+FcfQiTVSC7FmmbsatUPg.txt -a HSNIH-Palmer_true_snps.txt -k output/result.cXX.txt" + User time (seconds): 225.04 + System time (seconds): 110.63 + Percent of CPU this job got: 214% + Elapsed (wall clock) time (h:mm:ss or m:ss): 2:36.55 + Maximum resident set size (kbytes): 523876 ``` +Running the LMM takes only 2.5 minutes and uses less than 1GB RAM. + Now the goal is to try and crash the server before setting overcommit. |