*********************************************************************
* 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.16.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_11-cluster_5.16 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16 \
--annot all_da_open_results/train_models/clusters_11-cluster_5.16.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 23:18:37 2017
Read list of 316981 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.bim
Read 1 annotations for 316981 SNPs from all_da_open_results/train_models/clusters_11-cluster_5.16.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.bed
Estimating LD Score.
Reading list of 44710 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.16.snp
After merging with --print-snps, LD Scores for 37656 SNPs will be printed.
Writing LD Scores for 37656 SNPs to all_da_open_results/train_models/clusters_11-cluster_5.16.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_11-cluster_5.16.l2.ldscore.gz
         MAF       L2
mean  0.2370   0.3944
std   0.1437   1.0512
min   0.0051  -0.0823
25%   0.1115   0.0000
50%   0.2290   0.0223
75%   0.3589   0.2231
max   0.5000  13.1787

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000 -0.0122
L2  -0.0122  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    1296

Summary of Annotation Matrix Row Sums
count    316981.0000
mean          0.0041
std           0.0638
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Tue Oct 31 23:42:23 2017
Total time elapsed: 23.0m:45.76s