*********************************************************************
* 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.17.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_4-cluster_3.17 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17 \
--annot all_da_open_results/train_models/clusters_4-cluster_3.17.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 23:26:52 2017
Read list of 269222 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.bim
Read 1 annotations for 269222 SNPs from all_da_open_results/train_models/clusters_4-cluster_3.17.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.17.bed
Estimating LD Score.
Reading list of 38396 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.17.snp
After merging with --print-snps, LD Scores for 32315 SNPs will be printed.
Writing LD Scores for 32315 SNPs to all_da_open_results/train_models/clusters_4-cluster_3.17.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_4-cluster_3.17.l2.ldscore.gz
         MAF       L2
mean  0.2414   1.8969
std   0.1449   4.1446
min   0.0051  -0.1347
25%   0.1135   0.0207
50%   0.2352   0.3714
75%   0.3671   2.1165
max   0.5000  43.3994

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0784
L2   0.0784  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    4447

Summary of Annotation Matrix Row Sums
count    269222.0000
mean          0.0165
std           0.1275
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Wed Nov  1 00:11:50 2017
Total time elapsed: 44.0m:58.5s