*********************************************************************
* 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.1.snp \
--ld-wind-cm 1.0 \
--out all_da_open_results/train_models/clusters_11-cluster_5.1 \
--bfile /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1 \
--annot all_da_open_results/train_models/clusters_11-cluster_5.1.annot.gz \
--l2  

Beginning analysis at Tue Oct 31 17:27:10 2017
Read list of 779354 SNPs from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.bim
Read 1 annotations for 779354 SNPs from all_da_open_results/train_models/clusters_11-cluster_5.1.annot.gz
Read list of 489 individuals from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.fam
Reading genotypes from /net/gs/vol1/home/ajh24/bin/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.1.bed
Estimating LD Score.
Reading list of 116564 SNPs for which to print LD Scores from /net/gs/vol1/home/ajh24/bin/ldsc/hapmap3_snps/hm.1.snp
After merging with --print-snps, LD Scores for 98690 SNPs will be printed.
Writing LD Scores for 98690 SNPs to all_da_open_results/train_models/clusters_11-cluster_5.1.l2.ldscore.gz

Summary of LD Scores in all_da_open_results/train_models/clusters_11-cluster_5.1.l2.ldscore.gz
         MAF       L2
mean  0.2329   0.5731
std   0.1442   1.2315
min   0.0051  -0.0962
25%   0.1056   0.0121
50%   0.2219   0.1036
75%   0.3548   0.5514
max   0.5000  14.8287

MAF/LD Score Correlation Matrix
        MAF      L2
MAF  1.0000  0.0536
L2   0.0536  1.0000

Annotation Correlation Matrix
                         SPECIFIC_PEAK_INTERSECT
SPECIFIC_PEAK_INTERSECT                      1.0

Annotation Matrix Column Sums
SPECIFIC_PEAK_INTERSECT    4555

Summary of Annotation Matrix Row Sums
count    779354.0000
mean          0.0058
std           0.0762
min           0.0000
25%           0.0000
50%           0.0000
75%           0.0000
max           1.0000
Analysis finished at Tue Oct 31 19:41:29 2017
Total time elapsed: 2.0h:14.0m:19.28s