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solveblock
start_bp
end_bp
MWE (the first SNP is chr1 POS 58814)
using GhostKnockoffGWAS vcffile = "/oak/stanford/groups/zihuai/paisa/VCF/chr1.vcf.gz" chr = 1 start_bp = 1 end_bp = 10583 outdir = "/oak/stanford/groups/zihuai/paisa/LD_files" hg_build = 19 julia> solve_blocks(vcffile, chr, start_bp, end_bp, outdir, hg_build) ** On entry to DGETRI parameter number 6 had an illegal value ArgumentError: invalid argument #6 to LAPACK call Stacktrace: [1] chklapackerror @ /share/software/user/open/julia/1.9.0/share/julia/stdlib/v1.9/LinearAlgebra/src/lapack.jl:38 [inlined] [2] getri!(A::Matrix{Float64}, ipiv::Vector{Int64}) @ LinearAlgebra.LAPACK /share/software/user/open/julia/1.9.0/share/julia/stdlib/v1.9/LinearAlgebra/src/lapack.jl:1045 [3] inv! @ /share/software/user/open/julia/1.9.0/share/julia/stdlib/v1.9/LinearAlgebra/src/lu.jl:508 [inlined] [4] _inv(A::LinearAlgebra.Symmetric{Float64, Matrix{Float64}}) @ LinearAlgebra /share/software/user/open/julia/1.9.0/share/julia/stdlib/v1.9/LinearAlgebra/src/symmetric.jl:632 [5] inv @ /share/software/user/open/julia/1.9.0/share/julia/stdlib/v1.9/LinearAlgebra/src/symmetric.jl:648 [inlined] [6] choose_group_reps(Σ::LinearAlgebra.Symmetric{Float64, Matrix{Float64}}, groups::Vector{Int64}; threshold::Float64, prioritize_idx::Nothing, Σinv::Nothing) @ Knockoffs /home/groups/sabatti/.julia/packages/Knockoffs/AqvY6/src/group.jl:1974 [7] choose_group_reps @ /home/groups/sabatti/.julia/packages/Knockoffs/AqvY6/src/group.jl:1929 [inlined] [8] macro expansion @ /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/make_hdf5.jl:269 [inlined] [9] macro expansion @ ./timing.jl:393 [inlined] [10] solve_blocks(vcffile::String, chr::Int64, start_bp::Int64, end_bp::Int64, outdir::String, hg_build::Int64; snps_to_keep::Nothing, tol::Float64, min_maf::Float64, min_hwe::Float64, force_block_diag::Bool, method::String, linkage::String, force_contiguous::Bool, group_cor_cutoff::Float64, group_rep_cutoff::Float64, verbose::Bool) @ GhostKnockoffGWAS /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/make_hdf5.jl:266 [11] solve_blocks(vcffile::String, chr::Int64, start_bp::Int64, end_bp::Int64, outdir::String, hg_build::Int64) @ GhostKnockoffGWAS /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/make_hdf5.jl:228 [12] top-level scope @ In[94]:20
The text was updated successfully, but these errors were encountered:
handle case when no SNPs exist (#19)
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MWE (the first SNP is chr1 POS 58814)
The text was updated successfully, but these errors were encountered: