*********************************************************************
* 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_21-cluster_2.18 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.18 \
--annot all_da_open_results/train_models/clusters_21-cluster_2.18.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 23:41:42 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_21-cluster_2.18.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_21-cluster_2.18.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_21-cluster_2.18.l2.ldscore.gz
         MAF      L2
mean  0.2356  0.1232
std   0.1434  0.4113
min   0.0051 -0.0559
25%   0.1094  0.0000
50%   0.2249  0.0017
75%   0.3569  0.0430
max   0.5000  7.7172

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000 -0.0049
L2  -0.0049  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    477

Summary of Annotation Matrix Row Sums
count    285156.0000
mean          0.0017
std           0.0409
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Wed Nov  1 00:10:47 2017
Total time elapsed: 29.0m:4.44s