*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.0
* (C) 2014-2015 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
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Call: 
./ldsc.py \
--print-snps /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.5.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_5-cluster_5.5 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5 \
--annot all_da_open_results/train_models/clusters_5-cluster_5.5.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 18:43:13 2017
Read list of 633015 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.bim
Read 1 annotations for 633015 SNPs from all_da_open_results/train_models/clusters_5-cluster_5.5.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.5.bed
Estimating LD Score.
Reading list of 88059 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.5.snp
After merging with --print-snps, LD Scores for 74950 SNPs will be printed.
Writing LD Scores for 74950 SNPs to all_da_open_results/train_models/clusters_5-cluster_5.5.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_5-cluster_5.5.l2.ldscore.gz
         MAF       L2
mean  0.2353   0.3785
std   0.1428   0.8531
min   0.0051  -0.0701
25%   0.1104   0.0024
50%   0.2260   0.0493
75%   0.3558   0.2967
max   0.5000  11.7690

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0658
L2   0.0658  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    2307

Summary of Annotation Matrix Row Sums
count    633015.0000
mean          0.0036
std           0.0603
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Tue Oct 31 21:06:17 2017
Total time elapsed: 2.0h:23.0m:4.76s