********************************************************************* * LD Score Regression (LDSC) * Version 1.0.1 * (C) 2014-2019 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 /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/CUD_EUR-Johnson_2020.sumstats.gz \ --ref-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.EUR. \ --out /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/conditional/Human_Striatum_snATAC.conditional.CUD_EUR-Johnson_2020.EUR \ --w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC. \ --print-coefficients Beginning analysis at Mon Jun 24 14:56:19 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/CUD_EUR-Johnson_2020.sumstats.gz ... Read summary statistics for 1112777 SNPs. Reading reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.mergedReg2Map.EUR.,/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.EUR.[1-22] ... (ldscore_fromlist) Read reference panel LD Scores for 1198864 SNPs. Removing partitioned LD Scores with zero variance. Reading regression weight LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/1000G_ALL_Phase3_hg38_files/weights/1000G.EUR.weights.hm3_noMHC.[1-22] ... (ldscore_fromlist) Read regression weight LD Scores for 1198864 SNPs. After merging with reference panel LD, 1109925 SNPs remain. After merging with regression SNP LD, 1109925 SNPs remain. Removed 0 SNPs with chi^2 > 375.18 (1109925 SNPs remain) Total Observed scale h2: 0.0197 (0.0017) Categories: Human_Striatum_snATAC.Astro.hg38_0 Human_Striatum_snATAC.D1.D2H.hg38_1 Human_Striatum_snATAC.D1.Matrix.hg38_2 Human_Striatum_snATAC.D1.Striosome.hg38_3 Human_Striatum_snATAC.D2.Matrix.hg38_4 Human_Striatum_snATAC.D2.Striosome.hg38_5 Human_Striatum_snATAC.INT.hg38_6 Human_Striatum_snATAC.Microglia.hg38_7 Human_Striatum_snATAC.Oligo.hg38_8 Human_Striatum_snATAC.OPC.hg38_9 Human_Striatum_snATAC.mergedReg2Map_10 Coding_UCSCL2_11 Coding_UCSC.extend.500L2_11 Conserved_LindbladTohL2_11 Conserved_LindbladToh.extend.500L2_11 CTCF_HoffmanL2_11 CTCF_Hoffman.extend.500L2_11 DGF_ENCODEL2_11 DGF_ENCODE.extend.500L2_11 DHS_peaks_TrynkaL2_11 DHS_TrynkaL2_11 DHS_Trynka.extend.500L2_11 Enhancer_AnderssonL2_11 Enhancer_Andersson.extend.500L2_11 Enhancer_HoffmanL2_11 Enhancer_Hoffman.extend.500L2_11 FetalDHS_TrynkaL2_11 FetalDHS_Trynka.extend.500L2_11 H3K27ac_HniszL2_11 H3K27ac_Hnisz.extend.500L2_11 H3K27ac_PGC2L2_11 H3K27ac_PGC2.extend.500L2_11 H3K4me1_peaks_TrynkaL2_11 H3K4me1_TrynkaL2_11 H3K4me1_Trynka.extend.500L2_11 H3K4me3_peaks_TrynkaL2_11 H3K4me3_TrynkaL2_11 H3K4me3_Trynka.extend.500L2_11 H3K9ac_peaks_TrynkaL2_11 H3K9ac_TrynkaL2_11 H3K9ac_Trynka.extend.500L2_11 Intron_UCSCL2_11 Intron_UCSC.extend.500L2_11 PromoterFlanking_HoffmanL2_11 PromoterFlanking_Hoffman.extend.500L2_11 Promoter_UCSCL2_11 Promoter_UCSC.extend.500L2_11 Repressed_HoffmanL2_11 Repressed_Hoffman.extend.500L2_11 SuperEnhancer_HniszL2_11 SuperEnhancer_Hnisz.extend.500L2_11 TFBS_ENCODEL2_11 TFBS_ENCODE.extend.500L2_11 Transcr_HoffmanL2_11 Transcr_Hoffman.extend.500L2_11 TSS_HoffmanL2_11 TSS_Hoffman.extend.500L2_11 UTR_3_UCSCL2_11 UTR_3_UCSC.extend.500L2_11 UTR_5_UCSCL2_11 UTR_5_UCSC.extend.500L2_11 WeakEnhancer_HoffmanL2_11 WeakEnhancer_Hoffman.extend.500L2_11 Observed scale h2: -7.3229e-04 4.6888e-04 -3.3266e-03 1.5213e-03 -8.9166e-04 1.7371e-03 3.2980e-04 -1.3493e-03 -3.4635e-04 7.0433e-04 5.0086e-03 -2.0465e-03 -7.1628e-04 2.5940e-03 9.9344e-03 -5.1963e-04 3.4709e-04 1.5273e-03 -4.2963e-03 -6.5679e-03 2.9377e-03 1.7029e-02 -3.0905e-04 3.1211e-04 -1.9936e-04 -4.8052e-04 2.2484e-03 -5.5938e-03 -3.4020e-03 1.2499e-03 -2.8236e-03 -3.7640e-03 1.2507e-03 3.5816e-03 -7.4793e-03 1.2190e-04 -6.3344e-03 9.3047e-03 -4.4996e-05 3.1052e-03 -1.8963e-04 -1.0197e-03 1.3374e-03 5.5504e-04 -1.1657e-03 -2.1111e-03 3.0276e-03 -1.4238e-03 6.0146e-03 -1.8973e-02 1.8580e-02 2.2351e-03 -1.0985e-02 1.2570e-03 3.2575e-03 7.5398e-04 2.3387e-03 1.3716e-04 -2.3566e-04 3.1801e-05 -2.3078e-04 9.7316e-04 1.4526e-03 Observed scale h2 SE: 0.0009 0.0008 0.0022 0.0017 0.0021 0.0017 0.001 0.0007 0.0008 0.001 0.0031 0.0015 0.0019 0.0014 0.004 0.0013 0.0021 0.0032 0.0076 0.0039 0.0056 0.0096 0.0005 0.0008 0.0017 0.0024 0.0033 0.0054 0.0128 0.0137 0.0073 0.0078 0.0036 0.0079 0.0092 0.0016 0.0036 0.0045 0.0016 0.0036 0.0042 0.0118 0.0122 0.0007 0.0015 0.0035 0.0036 0.0054 0.0062 0.0179 0.0181 0.0033 0.0051 0.0041 0.007 0.0011 0.0016 0.0014 0.0015 0.0006 0.0011 0.0011 0.002 Proportion of SNPs: 0.0024 0.0016 0.0043 0.0032 0.0041 0.0031 0.0029 0.0019 0.0019 0.0024 0.0123 0.0026 0.0084 0.0041 0.0362 0.0022 0.0062 0.0149 0.0501 0.0135 0.02 0.0486 0.0004 0.0018 0.0044 0.0085 0.0104 0.0292 0.0364 0.0388 0.026 0.0314 0.0185 0.0434 0.0567 0.0042 0.0132 0.0232 0.0041 0.0131 0.022 0.0345 0.036 0.0008 0.003 0.0046 0.0055 0.0346 0.0553 0.0158 0.016 0.0136 0.0321 0.029 0.0616 0.0017 0.0031 0.0018 0.0035 0.0007 0.0031 0.0023 0.0085 Proportion of h2g: -0.0372 0.0238 -0.1688 0.0772 -0.0452 0.0881 0.0167 -0.0685 -0.0176 0.0357 0.2542 -0.1038 -0.0363 0.1316 0.5041 -0.0264 0.0176 0.0775 -0.218 -0.3333 0.1491 0.8641 -0.0157 0.0158 -0.0101 -0.0244 0.1141 -0.2838 -0.1726 0.0634 -0.1433 -0.191 0.0635 0.1817 -0.3795 0.0062 -0.3214 0.4722 -0.0023 0.1576 -0.0096 -0.0517 0.0679 0.0282 -0.0592 -0.1071 0.1536 -0.0722 0.3052 -0.9628 0.9428 0.1134 -0.5574 0.0638 0.1653 0.0383 0.1187 0.007 -0.012 0.0016 -0.0117 0.0494 0.0737 Enrichment: -15.2144 14.6313 -39.6629 23.8434 -11.0455 28.64 5.8001 -35.6673 -9.3517 14.9355 20.5891 -39.2759 -4.3176 32.1783 13.9105 -11.9726 2.8286 5.1887 -4.3509 -24.7196 7.4625 17.7961 -35.2991 8.7121 -2.3203 -2.8794 10.9526 -9.7123 -4.7449 1.6337 -5.5077 -6.0743 3.4267 4.1875 -6.6975 1.4578 -24.3204 20.3834 -0.5559 12.0311 -0.4364 -1.4994 1.8845 34.456 -19.9476 -23.3683 27.9459 -2.0878 5.5156 -60.9937 58.8444 8.3401 -17.3737 2.1988 2.6823 22.8498 38.4175 3.9393 -3.4343 2.1916 -3.8289 21.372 8.6315 Coefficients: -2.2643e-08 2.1775e-08 -5.9028e-08 3.5485e-08 -1.6438e-08 4.2623e-08 8.6320e-09 -5.3081e-08 -1.3918e-08 2.2228e-08 3.0642e-08 -5.8452e-08 -6.4257e-09 4.7889e-08 2.0702e-08 -1.7818e-08 4.2096e-09 7.7220e-09 -6.4752e-09 -3.6789e-08 1.1106e-08 2.6485e-08 -5.2533e-08 1.2966e-08 -3.4532e-09 -4.2853e-09 1.6300e-08 -1.4454e-08 -7.0615e-09 2.4314e-09 -8.1969e-09 -9.0400e-09 5.0997e-09 6.2320e-09 -9.9675e-09 2.1696e-09 -3.6195e-08 3.0335e-08 -8.2738e-10 1.7905e-08 -6.4948e-10 -2.2314e-09 2.8045e-09 5.1279e-08 -2.9687e-08 -3.4778e-08 4.1590e-08 -3.1072e-09 8.2085e-09 -9.0773e-08 8.7575e-08 1.2412e-08 -2.5856e-08 3.2723e-09 3.9919e-09 3.4006e-08 5.7174e-08 5.8627e-09 -5.1111e-09 3.2616e-09 -5.6983e-09 3.1807e-08 1.2846e-08 Coefficient SE: 2.8187e-08 3.7226e-08 3.8216e-08 3.8933e-08 3.8336e-08 4.0562e-08 2.6139e-08 2.6920e-08 3.2550e-08 3.2826e-08 1.8811e-08 4.1424e-08 1.7045e-08 2.5582e-08 8.3830e-09 4.5516e-08 2.5141e-08 1.6204e-08 1.1480e-08 2.2064e-08 2.1247e-08 1.4938e-08 7.6850e-08 3.4336e-08 3.0223e-08 2.1017e-08 2.3602e-08 1.3931e-08 2.6481e-08 2.6591e-08 2.1107e-08 1.8694e-08 1.4874e-08 1.3829e-08 1.2202e-08 2.8436e-08 2.0326e-08 1.4698e-08 3.0224e-08 2.0576e-08 1.4287e-08 2.5756e-08 2.5641e-08 6.4953e-08 3.7026e-08 5.7159e-08 4.9204e-08 1.1780e-08 8.4157e-09 8.5539e-08 8.5335e-08 1.8298e-08 1.1901e-08 1.0636e-08 8.5985e-09 5.1500e-08 3.9491e-08 5.7711e-08 3.3104e-08 6.0484e-08 2.8028e-08 3.5868e-08 1.7535e-08 Lambda GC: 1.127 Mean Chi^2: 1.1387 Intercept: 1.0004 (0.0071) Ratio: 0.0032 (0.0509) Analysis finished at Mon Jun 24 15:17:40 2024 Total time elapsed: 21.0m:20.49s