*********************************************************************
* 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.6.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_1-cluster_3.6 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6 \
--annot all_da_open_results/train_models/clusters_1-cluster_3.6.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 19:09:44 2017
Read list of 664016 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.bim
Read 1 annotations for 664016 SNPs from all_da_open_results/train_models/clusters_1-cluster_3.6.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.6.bed
Estimating LD Score.
Reading list of 91491 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.6.snp
After merging with --print-snps, LD Scores for 80218 SNPs will be printed.
Writing LD Scores for 80218 SNPs to all_da_open_results/train_models/clusters_1-cluster_3.6.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_1-cluster_3.6.l2.ldscore.gz
         MAF      L2
mean  0.2331  0.1025
std   0.1441  0.3524
min   0.0051 -0.0556
25%   0.1074  0.0000
50%   0.2219  0.0005
75%   0.3558  0.0338
max   0.5000  8.5761

MAF/LD Score Correlation Matrix
       MAF     L2
MAF  1.000  0.005
L2   0.005  1.000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    562

Summary of Annotation Matrix Row Sums
count    664016.0000
mean          0.0008
std           0.0291
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Tue Oct 31 21:32:09 2017
Total time elapsed: 2.0h:22.0m:24.2s