*********************************************************************
* 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.21.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_12-cluster_5.21 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21 \
--annot all_da_open_results/train_models/clusters_12-cluster_5.21.annot.gz \
--l2  

Beginning analysis at Wed Nov  1 00:07:22 2017
Read list of 138712 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.bim
Read 1 annotations for 138712 SNPs from all_da_open_results/train_models/clusters_12-cluster_5.21.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.21.bed
Estimating LD Score.
Reading list of 19331 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.21.snp
After merging with --print-snps, LD Scores for 16993 SNPs will be printed.
Writing LD Scores for 16993 SNPs to all_da_open_results/train_models/clusters_12-cluster_5.21.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_12-cluster_5.21.l2.ldscore.gz
         MAF      L2
mean  0.2398  0.0044
std   0.1429  0.0958
min   0.0051 -0.0159
25%   0.1155  0.0000
50%   0.2290  0.0000
75%   0.3640  0.0000
max   0.5000  3.8985

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0217
L2   0.0217  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    11

Summary of Annotation Matrix Row Sums
count    1.3871e+05
mean     7.9301e-05
std      8.9048e-03
min      0.0000e+00
25%      0.0000e+00
50%      0.0000e+00
75%      0.0000e+00
max      1.0000e+00
Analysis finished at Wed Nov  1 00:08:51 2017
Total time elapsed: 1.0m:28.56s