omiga --mode cis --genotype ../../liver --phenotype ../liver.apa.bed.gz --covariates liver_apa_ag.auto_covar --permutations 1000 --multiple-testing clipper --prefix liver_apa_omiga_qtl --gpu
Command Line Input:
--mode cis \
--genotype ../../liver \
--phenotype ../liver.apa.bed.gz \
--covariates liver_apa_ag.auto_covar \
--permutations 1000 \
--multiple-testing clipper \
--prefix liver_apa_omiga_qtl \
--gpu
Hostname: localhost.localdomain, CPU.threads: 1, MKL.threads: 1
Program start at: 2026-06-08T16:33:20.128
Loading phenotype file ...
Elapsed time: 7.302030426 seconds
Loaded (filtered) 302 samples, 10629 phenotypes
Loading covariates file ...
Elapsed time: 1.887632368 seconds
Loaded 302 samples, 20 covariates
Loading genotype file ...
* User provided major allele coding genotype or no variants with allele frequency > 0.5
[INFO] Eliminated 791 variants (338 with MAC < 6, 791 with MAF < 0.01 and 0 with Heterozygosity rate ≥ 0.99)
Elapsed time: 58.288738475 seconds
Loaded (filtered) 302 samples, 11681009 variants
* 21 covariates (including intercept) were used.
✅ Data loading completed.
Number of GRM specified: 0
Building GRM ...
Eigen decomposition ...
Elapsed time: 16.718583356 seconds
88.756842 seconds (413.78 M allocations: 18.649 GiB, 26.13% gc time, 16.23% compilation time: 19% of which was recompilation)
- MultipleTesting method: clipper
Chunk: 1/29, Chromosome: 1, start at: 2026-06-08T16:35:06.221
ERROR: ArgumentError: Illegal conversion of a CUDACore.DeviceMemory to a Ptr{Float32}
Stacktrace:
[1] convert(T::Type{Ptr{Float32}}, mem::CUDACore.DeviceMemory)
@ CUDACore ~/.julia/packages/CUDACore/sIGRL/lib/cudadrv/memory.jl:16
[2] convert(::Type{Ptr{Float32}}, managed::CUDACore.Managed{CUDACore.DeviceMemory})
@ CUDACore ~/.julia/packages/CUDACore/sIGRL/src/memory.jl:626
[3] unsafe_convert(typ::Type{Ptr{Float32}}, x::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory})
@ CUDACore ~/.julia/packages/CUDACore/sIGRL/src/array.jl:465
[4] gemm!(transA::Char, transB::Char, alpha::Float32, A::Matrix{Float32}, B::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory}, beta::Float32, C::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory})
@ LinearAlgebra.BLAS ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/blas.jl:1642
[5] gemm_wrapper!(C::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory}, tA::Char, tB::Char, A::Matrix{Float32}, B::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory}, α::Bool, β::Bool)
@ LinearAlgebra ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/matmul.jl:806
[6] _syrk_herk_gemm_wrapper!(C::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory}, tA::Char, tB::Char, A::Matrix{Float32}, B::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory}, α::Bool, β::Bool, ::Val{LinearAlgebra.BlasFlag.SYRK})
@ LinearAlgebra ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/matmul.jl:521
[7] generic_matmatmul_wrapper!(C::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory}, tA::Char, tB::Char, A::Matrix{Float32}, B::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory}, α::Bool, β::Bool, val::Val{LinearAlgebra.BlasFlag.SYRK})
@ LinearAlgebra ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/matmul.jl:507
[8] _mul!
@ ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/matmul.jl:328 [inlined]
[9] mul!
@ ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/matmul.jl:297 [inlined]
[10] mul!
@ ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/matmul.jl:265 [inlined]
[11] *
@ ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/matmul.jl:136 [inlined]
[12] _tri_matmul(A::Matrix{Float32}, B::LinearAlgebra.Adjoint{Float32, Matrix{Float32}}, C::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory}, δ::Nothing)
@ LinearAlgebra ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/matmul.jl:1279
[13] tri_matmul
@ ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/matmul.jl:1273 [inlined]
[14] *
@ ~/.julia/juliaup/julia-1.12.6+0.x64.linux.gnu/share/julia/stdlib/v1.12/LinearAlgebra/src/matmul.jl:1269 [inlined]
[15] residualizer_transform!(M_t::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory}, Q::Matrix{Float32}; center::Bool)
@ OmiGA ~/.julia/packages/OmiGA/lGPIq/src/MOLQTL.jl:273
[16] residualizer_transform!
@ ~/.julia/packages/OmiGA/lGPIq/src/MOLQTL.jl:269 [inlined]
[17] get_matrix_resid!(exppheno::CUDACore.CuArray{Float32, 2, CUDACore.DeviceMemory}, Q::Matrix{Float32}; return_std::Bool, center::Bool)
@ OmiGA ~/.julia/packages/OmiGA/lGPIq/src/MOLQTL.jl:337
[18] runOmiGA_cis(struct_PHENO:😮miGA.Phenotype{Float32}, _struct_GENO:😮miGA.Genotype{UInt8}, _struct_KIN:😮miGA.Kinship{Float32}, _struct_COVAR:😮miGA.Covariates{Float32}, _struct_PRIOR_HerB::Nothing; _struct_DOM::Nothing, _struct_ITERM::Nothing)
@ OmiGA ~/.julia/packages/OmiGA/lGPIq/src/QTL_cis.jl:457
[19] real_main(ARGS::Vector{String})
@ OmiGA ~/.julia/packages/OmiGA/lGPIq/src/OmiGA.jl:289
[20] main(ARGS::Vector{String})
@ OmiGA ~/.julia/packages/OmiGA/lGPIq/src/OmiGA.jl:79
[21] _start()
@ Base ./client.jl:556