*********************************************************************
* 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.11.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_5-cluster_2.11 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11 \
--annot all_da_open_results/train_models/clusters_5-cluster_2.11.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 21:32:58 2017
Read list of 493922 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.bim
Read 1 annotations for 493922 SNPs from all_da_open_results/train_models/clusters_5-cluster_2.11.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.11.bed
Estimating LD Score.
Reading list of 71092 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.11.snp
After merging with --print-snps, LD Scores for 61027 SNPs will be printed.
Writing LD Scores for 61027 SNPs to all_da_open_results/train_models/clusters_5-cluster_2.11.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_5-cluster_2.11.l2.ldscore.gz
         MAF       L2
mean  0.2389   1.3516
std   0.1430   2.4512
min   0.0051  -0.1145
25%   0.1145   0.0844
50%   0.2301   0.4408
75%   0.3609   1.5873
max   0.5000  23.3706

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0365
L2   0.0365  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    5695

Summary of Annotation Matrix Row Sums
count    493922.0000
mean          0.0115
std           0.1068
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Wed Nov  1 00:22:21 2017
Total time elapsed: 2.0h:49.0m:23.03s