*********************************************************************
* 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.22.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_12-cluster_1.22 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22 \
--annot all_da_open_results/train_models/clusters_12-cluster_1.22.annot.gz \
--l2  

Beginning analysis at Wed Nov  1 00:12:18 2017
Read list of 141123 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.bim
Read 1 annotations for 141123 SNPs from all_da_open_results/train_models/clusters_12-cluster_1.22.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.22.bed
Estimating LD Score.
Reading list of 20106 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.22.snp
After merging with --print-snps, LD Scores for 17261 SNPs will be printed.
Writing LD Scores for 17261 SNPs to all_da_open_results/train_models/clusters_12-cluster_1.22.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_12-cluster_1.22.l2.ldscore.gz
         MAF       L2
mean  0.2359   1.3578
std   0.1442   2.3495
min   0.0051  -0.1216
25%   0.1084   0.0000
50%   0.2280   0.1752
75%   0.3579   1.7178
max   0.5000  15.9037

MAF/LD Score Correlation Matrix
      MAF    L2
MAF  1.00  0.08
L2   0.08  1.00

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    1843

Summary of Annotation Matrix Row Sums
count    141123.0000
mean          0.0131
std           0.1135
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Wed Nov  1 00:22:07 2017
Total time elapsed: 9.0m:48.82s