*********************************************************************
* 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.20.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_26-cluster_1.20 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20 \
--annot all_da_open_results/train_models/clusters_26-cluster_1.20.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 23:57:20 2017
Read list of 221626 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.bim
Read 1 annotations for 221626 SNPs from all_da_open_results/train_models/clusters_26-cluster_1.20.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.20.bed
Estimating LD Score.
Reading list of 36301 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.20.snp
After merging with --print-snps, LD Scores for 31359 SNPs will be printed.
Writing LD Scores for 31359 SNPs to all_da_open_results/train_models/clusters_26-cluster_1.20.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_26-cluster_1.20.l2.ldscore.gz
         MAF      L2
mean  0.2336  0.1620
std   0.1437  0.5340
min   0.0051 -0.0720
25%   0.1063  0.0000
50%   0.2219  0.0000
75%   0.3569  0.0489
max   0.5000  6.7477

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0589
L2   0.0589  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    408

Summary of Annotation Matrix Row Sums
count    221626.0000
mean          0.0018
std           0.0429
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Wed Nov  1 00:08:37 2017
Total time elapsed: 11.0m:17.57s