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-rw-r--r--issues/gemma/HS-Rat-crashes-gemma.gmi25
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.