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* 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
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Call: 
./ldsc.py \
--h2-cts /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/OD_vs_UX_AFR-Polimanti_2020.sumstats.gz \
--ref-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/snATAC_cross_species_caudate/data/tidy_data/ldsc_gwas/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.AFR. \
--out /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/enrichments/Human_Striatum_snATAC.OD_vs_UX_AFR-Polimanti_2020.AFR \
--ref-ld-chr-cts /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/Human_Striatum_snATAC.AFR_hg38.ldcts \
--w-ld-chr /projects/pfenninggroup/machineLearningForComputationalBiology/snATAC_cross_species_caudate/data/tidy_data/ldsc_gwas/1000G_ALL_Phase3_hg38_files/weights/1000G.AFR.weights.hm3_noMHC. 

Beginning analysis at Sat Jun 22 15:08:38 2024
Reading summary statistics from /projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/gwas/munged/OD_vs_UX_AFR-Polimanti_2020.sumstats.gz ...
Read summary statistics for 978488 SNPs.
Reading reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/snATAC_cross_species_caudate/data/tidy_data/ldsc_gwas/1000G_ALL_Phase3_hg38_files/baseline_v1.1/baseline_v1.1.AFR.[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1192221 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/snATAC_cross_species_caudate/data/tidy_data/ldsc_gwas/1000G_ALL_Phase3_hg38_files/weights/1000G.AFR.weights.hm3_noMHC.[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1192221 SNPs.
After merging with reference panel LD, 975573 SNPs remain.
After merging with regression SNP LD, 975573 SNPs remain.
Removed 0 SNPs with chi^2 > 80 (975573 SNPs remain)
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Astro.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.AFR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.D2H.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.AFR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Matrix.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.AFR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D1.Striosome.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.AFR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Matrix.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.AFR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.D2.Striosome.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.AFR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.INT.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.AFR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Microglia.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.AFR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.Oligo.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.AFR.[1-22] ... (ldscore_fromlist)
Performing regression.
Reading cts reference panel LD Score from /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.OPC.hg38.AFR.,/projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/annotations/Human_Striatum_snATAC.merged.AFR.[1-22] ... (ldscore_fromlist)
Performing regression.
Results printed to /projects/pfenninggroup/machineLearningForComputationalBiology/StriatumComparativeGenomics/data/tidy_data/human_Str_ldsc/enrichments/Human_Striatum_snATAC.OD_vs_UX_AFR-Polimanti_2020.AFR.cell_type_results.txt
Analysis finished at Sat Jun 22 16:27:31 2024
Total time elapsed: 1.0h:18.0m:53.28s