********************************************************************* * 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/deepika_pain_gwas/KneePain-Kupari_2021.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.KneePain-Kupari_2021.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 14:56:21 2024 Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/deepika_pain_gwas/KneePain-Kupari_2021.sumstats.gz ... Read summary statistics for 1066158 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, 1056555 SNPs remain. After merging with regression SNP LD, 1056555 SNPs remain. Removed 0 SNPs with chi^2 > 232.062 (1056555 SNPs remain) Total Observed scale h2: 0.0989 (0.0041) 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: 1.5464e-03 3.3344e-03 1.1741e-03 5.6464e-04 6.9331e-03 1.8835e-03 -2.3839e-04 1.4035e-03 8.6954e-05 1.9695e-03 -2.9064e-03 -4.3861e-03 -7.5818e-03 1.3385e-02 2.8407e-02 -5.7464e-03 5.4789e-03 7.2131e-03 2.0982e-03 -1.3399e-02 -1.4498e-02 2.0839e-02 1.2191e-04 -7.0282e-04 -1.3445e-03 5.3898e-03 5.8660e-03 2.4959e-03 2.4177e-02 -4.0638e-02 -1.0876e-02 -6.1048e-03 -1.7156e-03 -8.7844e-03 3.3354e-02 -2.2038e-03 7.4849e-03 -1.6226e-03 8.0269e-03 -8.6950e-03 1.8499e-02 -1.9166e-02 1.8723e-02 -1.0417e-03 -3.7150e-03 -9.1332e-03 1.0656e-02 8.5249e-03 -5.9799e-03 -4.0714e-02 3.9980e-02 2.7801e-04 2.6405e-03 4.1529e-03 2.3193e-02 1.1491e-03 2.2477e-03 3.7362e-03 -4.3521e-03 1.6451e-04 -4.2445e-03 2.9688e-03 -1.5053e-03 Observed scale h2 SE: 0.0017 0.0016 0.0045 0.0035 0.0044 0.0034 0.0023 0.0016 0.0017 0.0021 0.0065 0.0028 0.0043 0.0036 0.0072 0.0025 0.0047 0.0068 0.0163 0.009 0.0111 0.018 0.001 0.0018 0.004 0.0053 0.0068 0.0124 0.0254 0.0277 0.0132 0.0152 0.0076 0.0188 0.0242 0.0042 0.0074 0.0088 0.0032 0.0074 0.0095 0.0221 0.0232 0.0018 0.0037 0.0068 0.0073 0.0112 0.0155 0.0377 0.0378 0.0065 0.0115 0.0089 0.0146 0.0021 0.0032 0.0021 0.0024 0.0011 0.0024 0.0024 0.004 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: 0.0156 0.0337 0.0119 0.0057 0.0701 0.0191 -0.0024 0.0142 0.0009 0.0199 -0.0294 -0.0444 -0.0767 0.1354 0.2874 -0.0581 0.0554 0.073 0.0212 -0.1355 -0.1467 0.2108 0.0012 -0.0071 -0.0136 0.0545 0.0593 0.0252 0.2446 -0.4111 -0.11 -0.0618 -0.0174 -0.0889 0.3374 -0.0223 0.0757 -0.0164 0.0812 -0.088 0.1871 -0.1939 0.1894 -0.0105 -0.0376 -0.0924 0.1078 0.0862 -0.0605 -0.4119 0.4045 0.0028 0.0267 0.042 0.2346 0.0116 0.0227 0.0378 -0.044 0.0017 -0.0429 0.03 -0.0152 Enrichment: 6.4051 20.7433 2.7908 1.7642 17.1217 6.1908 -0.8358 7.3962 0.4681 8.3262 -2.3819 -16.7812 -9.1112 33.1013 7.9298 -26.3956 8.9014 4.8854 0.4236 -10.0537 -7.3418 4.3416 2.7758 -3.9111 -3.1198 6.4388 5.6968 0.8639 6.7226 -10.5897 -4.2294 -1.9641 -0.9371 -2.0475 5.9544 -5.2543 5.7291 -0.7086 19.7721 -6.7163 8.4874 -5.6184 5.2593 -12.8917 -12.674 -20.1545 19.6077 2.4922 -1.0932 -26.0932 25.2435 0.2068 0.8326 1.4483 3.8072 6.9424 7.361 21.3921 -12.6444 2.2602 -14.039 12.9979 -1.7832 Coefficients: 4.7814e-08 1.5485e-07 2.0834e-08 1.3170e-08 1.2782e-07 4.6215e-08 -6.2394e-09 5.5214e-08 3.4941e-09 6.2156e-08 -1.7781e-08 -1.2527e-07 -6.8016e-08 2.4710e-07 5.9197e-08 -1.9705e-07 6.6450e-08 3.6470e-08 3.1623e-09 -7.5052e-08 -5.4807e-08 3.2410e-08 2.0722e-08 -2.9197e-08 -2.3289e-08 4.8066e-08 4.2527e-08 6.4492e-09 5.0185e-08 -7.9053e-08 -3.1573e-08 -1.4662e-08 -6.9956e-09 -1.5285e-08 4.4450e-08 -3.9224e-08 4.2769e-08 -5.2900e-09 1.4760e-07 -5.0138e-08 6.3360e-08 -4.1942e-08 3.9261e-08 -9.6238e-08 -9.4612e-08 -1.5046e-07 1.4637e-07 1.8604e-08 -8.1611e-09 -1.9479e-07 1.8844e-07 1.5439e-09 6.2153e-09 1.0811e-08 2.8421e-08 5.1825e-08 5.4950e-08 1.5969e-07 -9.4391e-08 1.6873e-08 -1.0480e-07 9.7031e-08 -1.3312e-08 Coefficient SE: 5.2753e-08 7.4766e-08 8.0669e-08 8.1778e-08 8.1630e-08 8.2522e-08 6.0395e-08 6.4494e-08 6.9590e-08 6.7796e-08 3.9659e-08 8.1138e-08 3.8447e-08 6.6397e-08 1.5090e-08 8.4912e-08 5.6500e-08 3.4580e-08 2.4555e-08 5.0217e-08 4.1963e-08 2.7940e-08 1.7279e-07 7.4579e-08 6.8801e-08 4.7227e-08 4.9111e-08 3.2093e-08 5.2691e-08 5.3946e-08 3.8242e-08 3.6481e-08 3.0849e-08 3.2653e-08 3.2235e-08 7.4119e-08 4.2073e-08 2.8664e-08 5.8955e-08 4.2918e-08 3.2399e-08 4.8405e-08 4.8562e-08 1.6678e-07 9.5341e-08 1.1192e-07 1.0057e-07 2.4350e-08 2.1113e-08 1.8043e-07 1.7804e-07 3.6100e-08 2.6994e-08 2.3126e-08 1.7928e-08 9.3580e-08 7.9235e-08 8.8529e-08 5.3054e-08 1.1480e-07 5.8698e-08 7.8290e-08 3.5448e-08 Lambda GC: 1.3685 Mean Chi^2: 1.4553 Intercept: 1.0145 (0.0087) Ratio: 0.0318 (0.0191) Analysis finished at Mon Jun 24 15:12:47 2024 Total time elapsed: 16.0m:26.53s