*********************************************************************
* 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.3.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_5-cluster_2.3 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3 \
--annot all_da_open_results/train_models/clusters_5-cluster_2.3.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 17:27:53 2017
Read list of 706350 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.bim
Read 1 annotations for 706350 SNPs from all_da_open_results/train_models/clusters_5-cluster_2.3.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.3.bed
Estimating LD Score.
Reading list of 96664 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.3.snp
After merging with --print-snps, LD Scores for 83286 SNPs will be printed.
Writing LD Scores for 83286 SNPs to all_da_open_results/train_models/clusters_5-cluster_2.3.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_5-cluster_2.3.l2.ldscore.gz
         MAF       L2
mean  0.2395   1.1974
std   0.1436   1.7773
min   0.0051  -0.1211
25%   0.1145   0.1159
50%   0.2311   0.5046
75%   0.3630   1.4977
max   0.5000  18.1503

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0855
L2   0.0855  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    7515

Summary of Annotation Matrix Row Sums
count    706350.0000
mean          0.0106
std           0.1026
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Tue Oct 31 20:08:07 2017
Total time elapsed: 2.0h:40.0m:14.19s