*********************************************************************
* 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.18.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_5-cluster_3.18 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18 \
--annot all_da_open_results/train_models/clusters_5-cluster_3.18.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 23:39:35 2017
Read list of 285156 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.bim
Read 1 annotations for 285156 SNPs from all_da_open_results/train_models/clusters_5-cluster_3.18.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18.bed
Estimating LD Score.
Reading list of 40891 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.18.snp
After merging with --print-snps, LD Scores for 35326 SNPs will be printed.
Writing LD Scores for 35326 SNPs to all_da_open_results/train_models/clusters_5-cluster_3.18.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_5-cluster_3.18.l2.ldscore.gz
         MAF       L2
mean  0.2356   0.7025
std   0.1434   1.2903
min   0.0051  -0.0951
25%   0.1094   0.0201
50%   0.2249   0.1858
75%   0.3569   0.8019
max   0.5000  13.4859

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0674
L2   0.0674  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    2276

Summary of Annotation Matrix Row Sums
count    285156.000
mean          0.008
std           0.089
min           0.000
25%           0.000
50%           0.000
75%           0.000
max           1.000
Analysis finished at Wed Nov  1 00:12:12 2017
Total time elapsed: 32.0m:37.77s