*********************************************************************
* 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.9.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_12-cluster_5.9 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9 \
--annot all_da_open_results/train_models/clusters_12-cluster_5.9.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 20:58:28 2017
Read list of 438106 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.bim
Read 1 annotations for 438106 SNPs from all_da_open_results/train_models/clusters_12-cluster_5.9.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.9.bed
Estimating LD Score.
Reading list of 63706 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.9.snp
After merging with --print-snps, LD Scores for 55885 SNPs will be printed.
Writing LD Scores for 55885 SNPs to all_da_open_results/train_models/clusters_12-cluster_5.9.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_12-cluster_5.9.l2.ldscore.gz
         MAF      L2
mean  0.2343  0.0070
std   0.1436  0.0909
min   0.0051 -0.0154
25%   0.1084  0.0000
50%   0.2239  0.0000
75%   0.3558  0.0000
max   0.5000  3.4810

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000 -0.0346
L2  -0.0346  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    33

Summary of Annotation Matrix Row Sums
count    4.3811e+05
mean     7.5324e-05
std      8.6786e-03
min      0.0000e+00
25%      0.0000e+00
50%      0.0000e+00
75%      0.0000e+00
max      1.0000e+00
Analysis finished at Tue Oct 31 21:03:45 2017
Total time elapsed: 5.0m:16.51s