*********************************************************************
* 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.2.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_5-cluster_4.2 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2 \
--annot all_da_open_results/train_models/clusters_5-cluster_4.2.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 17:26:35 2017
Read list of 839590 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.bim
Read 1 annotations for 839590 SNPs from all_da_open_results/train_models/clusters_5-cluster_4.2.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.2.bed
Estimating LD Score.
Reading list of 116575 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.2.snp
After merging with --print-snps, LD Scores for 100038 SNPs will be printed.
Writing LD Scores for 100038 SNPs to all_da_open_results/train_models/clusters_5-cluster_4.2.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_5-cluster_4.2.l2.ldscore.gz
         MAF       L2
mean  0.2371   0.8212
std   0.1439   1.3297
min   0.0051  -0.0931
25%   0.1115   0.0718
50%   0.2280   0.2877
75%   0.3609   1.0000
max   0.5000  17.9141

MAF/LD Score Correlation Matrix
       MAF     L2
MAF  1.000  0.076
L2   0.076  1.000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    6049

Summary of Annotation Matrix Row Sums
count    839590.0000
mean          0.0072
std           0.0846
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Tue Oct 31 19:02:52 2017
Total time elapsed: 1.0h:36.0m:17.83s