*********************************************************************
* 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.19.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_5-cluster_3.19 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19 \
--annot all_da_open_results/train_models/clusters_5-cluster_3.19.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 23:49:04 2017
Read list of 232363 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.bim
Read 1 annotations for 232363 SNPs from all_da_open_results/train_models/clusters_5-cluster_3.19.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.19.bed
Estimating LD Score.
Reading list of 26259 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.19.snp
After merging with --print-snps, LD Scores for 21991 SNPs will be printed.
Writing LD Scores for 21991 SNPs to all_da_open_results/train_models/clusters_5-cluster_3.19.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_5-cluster_3.19.l2.ldscore.gz
         MAF       L2
mean  0.2369   0.5049
std   0.1428   1.0305
min   0.0051  -0.0958
25%   0.1125   0.0117
50%   0.2331   0.1001
75%   0.3569   0.5131
max   0.5000  12.6011

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0556
L2   0.0556  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    1419

Summary of Annotation Matrix Row Sums
count    232363.0000
mean          0.0061
std           0.0779
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Wed Nov  1 00:22:26 2017
Total time elapsed: 33.0m:22.07s