*********************************************************************
* 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 \
--h2 ldsc.sumstats.gz \
--ref-ld-chr 1000G_Phase3_cell_type_groups/cell_type_group.3.,baseline_v1.1/baseline. \
--out ldsc_CNS \
--overlap-annot  \
--frqfile-chr 1000G_Phase3_frq/1000G.EUR.QC. \
--w-ld-chr 1000G_Phase3_weights_hm3_no_MHC/weights.hm3_noMHC. \
--print-coefficients  

Beginning analysis at Sat Jun 23 09:46:17 2018
Reading summary statistics from ldsc.sumstats.gz ...
Read summary statistics for 1025112 SNPs.
Reading reference panel LD Score from 1000G_Phase3_cell_type_groups/cell_type_group.3.,baseline_v1.1/baseline.[1-22] ...
Read reference panel LD Scores for 1190321 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from 1000G_Phase3_weights_hm3_no_MHC/weights.hm3_noMHC.[1-22] ...
Read regression weight LD Scores for 1187349 SNPs.
After merging with reference panel LD, 1016832 SNPs remain.
After merging with regression SNP LD, 1014419 SNPs remain.
Removed 15 SNPs with chi^2 > 795.64 (1014404 SNPs remain)
Total Observed scale h2: 0.162 (0.0051)
Categories: L2_0 baseL2_1 Coding_UCSC.bedL2_1 Coding_UCSC.extend.500.bedL2_1 Conserved_LindbladToh.bedL2_1 Conserved_LindbladToh.extend.500.bedL2_1 CTCF_Hoffman.bedL2_1 CTCF_Hoffman.extend.500.bedL2_1 DGF_ENCODE.bedL2_1 DGF_ENCODE.extend.500.bedL2_1 DHS_peaks_Trynka.bedL2_1 DHS_Trynka.bedL2_1 DHS_Trynka.extend.500.bedL2_1 Enhancer_Andersson.bedL2_1 Enhancer_Andersson.extend.500.bedL2_1 Enhancer_Hoffman.bedL2_1 Enhancer_Hoffman.extend.500.bedL2_1 FetalDHS_Trynka.bedL2_1 FetalDHS_Trynka.extend.500.bedL2_1 H3K27ac_Hnisz.bedL2_1 H3K27ac_Hnisz.extend.500.bedL2_1 H3K27ac_PGC2.bedL2_1 H3K27ac_PGC2.extend.500.bedL2_1 H3K4me1_peaks_Trynka.bedL2_1 H3K4me1_Trynka.bedL2_1 H3K4me1_Trynka.extend.500.bedL2_1 H3K4me3_peaks_Trynka.bedL2_1 H3K4me3_Trynka.bedL2_1 H3K4me3_Trynka.extend.500.bedL2_1 H3K9ac_peaks_Trynka.bedL2_1 H3K9ac_Trynka.bedL2_1 H3K9ac_Trynka.extend.500.bedL2_1 Intron_UCSC.bedL2_1 Intron_UCSC.extend.500.bedL2_1 PromoterFlanking_Hoffman.bedL2_1 PromoterFlanking_Hoffman.extend.500.bedL2_1 Promoter_UCSC.bedL2_1 Promoter_UCSC.extend.500.bedL2_1 Repressed_Hoffman.bedL2_1 Repressed_Hoffman.extend.500.bedL2_1 SuperEnhancer_Hnisz.bedL2_1 SuperEnhancer_Hnisz.extend.500.bedL2_1 TFBS_ENCODE.bedL2_1 TFBS_ENCODE.extend.500.bedL2_1 Transcribed_Hoffman.bedL2_1 Transcribed_Hoffman.extend.500.bedL2_1 TSS_Hoffman.bedL2_1 TSS_Hoffman.extend.500.bedL2_1 UTR_3_UCSC.bedL2_1 UTR_3_UCSC.extend.500.bedL2_1 UTR_5_UCSC.bedL2_1 UTR_5_UCSC.extend.500.bedL2_1 WeakEnhancer_Hoffman.bedL2_1 WeakEnhancer_Hoffman.extend.500.bedL2_1
Lambda GC: 2.5641
Mean Chi^2: 3.4336
Intercept: 1.0872 (0.0225)
Ratio: 0.0358 (0.0093)
Reading annot matrix from 1000G_Phase3_cell_type_groups/cell_type_group.3.,baseline_v1.1/baseline.[1-22] ...
Results printed to ldsc_CNS.results
Analysis finished at Sat Jun 23 09:48:01 2018
Total time elapsed: 1.0m:43.6s