*********************************************************************
* 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
*********************************************************************
Call: 
./ldsc.py \
--print-snps /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.7.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_1-cluster_1.7 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7 \
--annot all_da_open_results/train_models/clusters_1-cluster_1.7.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 19:40:48 2017
Read list of 589569 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.bim
Read 1 annotations for 589569 SNPs from all_da_open_results/train_models/clusters_1-cluster_1.7.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.7.bed
Estimating LD Score.
Reading list of 75316 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.7.snp
After merging with --print-snps, LD Scores for 65848 SNPs will be printed.
Writing LD Scores for 65848 SNPs to all_da_open_results/train_models/clusters_1-cluster_1.7.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_1-cluster_1.7.l2.ldscore.gz
         MAF      L2
mean  0.2376  0.1269
std   0.1437  0.3578
min   0.0051 -0.0365
25%   0.1104  0.0000
50%   0.2290  0.0115
75%   0.3609  0.0746
max   0.5000  6.4028

MAF/LD Score Correlation Matrix
       MAF     L2
MAF  1.000  0.032
L2   0.032  1.000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    698

Summary of Annotation Matrix Row Sums
count    589569.0000
mean          0.0012
std           0.0344
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Tue Oct 31 21:48:43 2017
Total time elapsed: 2.0h:7.0m:54.97s