*********************************************************************
* 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.16.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_5-cluster_6.16 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16 \
--annot all_da_open_results/train_models/clusters_5-cluster_6.16.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 23:15:11 2017
Read list of 316981 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.bim
Read 1 annotations for 316981 SNPs from all_da_open_results/train_models/clusters_5-cluster_6.16.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.16.bed
Estimating LD Score.
Reading list of 44710 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.16.snp
After merging with --print-snps, LD Scores for 37656 SNPs will be printed.
Writing LD Scores for 37656 SNPs to all_da_open_results/train_models/clusters_5-cluster_6.16.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_5-cluster_6.16.l2.ldscore.gz
         MAF       L2
mean  0.2370   0.3806
std   0.1437   0.9325
min   0.0051  -0.0855
25%   0.1115   0.0017
50%   0.2290   0.0475
75%   0.3589   0.2709
max   0.5000  15.6822

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0335
L2   0.0335  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    1254

Summary of Annotation Matrix Row Sums
count    316981.0000
mean          0.0040
std           0.0628
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Wed Nov  1 00:12:52 2017
Total time elapsed: 57.0m:40.7s