Error: MethodError(Matrix{<:Unsigned}

[ccbvib]

I am apply Baysor to Resolve data. The "preview" step works, and outputs the HTML report, which looks fine, but the "run" step crashes with the following error. Any idea what is going on here?

[17:26:42] Info: Processing complete. [17:26:50] Info: Estimating local colors [17:27:29] Info: Saving results to /staging/leuven/stg_00104/vsc/Projects/Project_Theo/resolve/output/segmentation.csv [17:27:32] Info: Plot diagnostics [17:28:33] Info: Estimating boundary polygons [17:30:16] Error: MethodError(Matrix{<:Unsigned}, (Matrix{Int64}(undef, 0, 0),), 0x0000000000007b7d) |
| convert(#unused#::Type{Matrix{<:Unsigned}}, a::Matrix{Int64}) at array.jl:554 | find_grid_point_labels_kde(pos_data::Matrix{Float64}, cell_labels::Vector{Int64}, min_x::Vector{Float64}, max_x::Vector{Float64}; grid_step ::Float64, bandwidth::Float64, dens_threshold::Float64, min_molecules_per_cell::Int64, verbose::Bool) at boundary_estimation.jl:165 | (::Baysor.var"#find_grid_point_labels_kde##kw")(::NamedTuple{(:grid_step, :bandwidth), Tuple{Float64, Float64}}, ::typeof(Baysor.find_grid_ point_labels_kde), pos_data::Matrix{Float64}, cell_labels::Vector{Int64}, min_x::Vector{Float64}, max_x::Vector{Float64}) at boundary_estimation.jl:159 | boundary_polygons(pos_data::Matrix{Float64}, cell_labels::Vector{Int64}; min_x::Nothing, max_x::Nothing, grid_step::Float64, min_border_len gth::Int64, shape_method::Symbol, max_dev::Float64, bandwidth::Float64, exclude_labels::Vector{Int64}, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTupl e{(), Tuple{}}}) at boundary_estimation.jl:263 | boundary_polygons at boundary_estimation.jl:254 [inlined] | #boundary_polygons#214 at boundary_estimation.jl:248 [inlined] | (::Baysor.var"#boundary_polygons##kw")(::NamedTuple{(:grid_step, :bandwidth), Tuple{Float64, Float64}}, ::typeof(Baysor.boundary_polygons), spatial_df::DataFrames.DataFrame, args::Vector{Int64}) at boundary_estimation.jl:248 | (::Baysor.var"#333#337"{DataFrames.DataFrame, Vector{Int64}, Dict{String, Any}, Float64})(mask::BitVector) at main.jl:220 | (::ProgressMeter.var"#56#59"{Distributed.RemoteChannel{Channel{Bool}}, Baysor.var"#333#337"{DataFrames.DataFrame, Vector{Int64}, Dict{Strin g, Any}, Float64}})(x::BitVector) at ProgressMeter.jl:1018 | iterate at generator.jl:47 [inlined] | _collect(c::Vector{BitVector}, itr::Base.Generator{Vector{BitVector}, ProgressMeter.var"#56#59"{Distributed.RemoteChannel{Channel{Bool}}, B aysor.var"#333#337"{DataFrames.DataFrame, Vector{Int64}, Dict{String, Any}, Float64}}}, #unused#::Base.EltypeUnknown, isz::Base.HasShape{1}) at array.jl:744 | collect_similar(cont::Vector{BitVector}, itr::Base.Generator{Vector{BitVector}, ProgressMeter.var"#56#59"{Distributed.RemoteChannel{Channel {Bool}}, Baysor.var"#333#337"{DataFrames.DataFrame, Vector{Int64}, Dict{String, Any}, Float64}}}) at array.jl:653 | map(f::Function, A::Vector{BitVector}) at abstractarray.jl:2849 | macro expansion at ProgressMeter.jl:1017 [inlined] | macro expansion at task.jl:399 [inlined] | macro expansion at ProgressMeter.jl:1016 [inlined] | macro expansion at task.jl:399 [inlined] | progress_map(::Function, ::Vararg{Any}; mapfun::Function, progress::ProgressMeter.Progress, channel_bufflen::Int64, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) at ProgressMeter.jl:1009 | progress_map(::Function, ::Vararg{Any}) at ProgressMeter.jl:1005 | plot_transcript_assignment_panel(df_res::DataFrames.DataFrame, assignment::Vector{Int64}, args::Dict{String, Any}; clusters::Vector{Int64}, prior_polygons::Vector{Matrix{Float64}}, gene_colors::Vector{ColorTypes.Lab{Float64}}) at main.jl:220 | (::Baysor.var"#plot_transcript_assignment_panel##kw")(::NamedTuple{(:clusters, :prior_polygons, :gene_colors), Tuple{Vector{Int64}, Vector{Matrix{Float64}}, Vector{ColorTypes.Lab{Float64}}}}, ::typeof(Baysor.plot_transcript_assignment_panel), df_res::DataFrames.DataFrame, assignment::Vector{Int64}, args::Dict{String, Any}) at main.jl:205 | save_segmentation_results(bm_data::Baysor.BmmData{3}, gene_names::Vector{String}, args::Dict{String, Any}; mol_clusts::NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, comp_segs::Nothing, prior_polygons::Vector{Matrix{Float64}}) at main.jl:414 | (::Baysor.var"#save_segmentation_results##kw")(::NamedTuple{(:mol_clusts, :comp_segs, :prior_polygons), Tuple{NamedTuple{(:exprs, :assignment, :diffs, :assignment_probs, :change_fracs), Tuple{Matrix{Float64}, Vector{Int64}, Vector{Float64}, Matrix{Float64}, Vector{Float64}}}, Nothing, Vector{Matrix{Float64}}}}, ::typeof(Baysor.save_segmentation_results), bm_data::Baysor.BmmData{3}, gene_names::Vector{String}, args::Dict{String, Any}) at main.jl:394 | run_cli_main(args::Vector{String}) at main.jl:481 | run_cli(args::Vector{String}) at common.jl:152 | run_cli at common.jl:137 [inlined] | julia_main() at common.jl:177 | top-level scope at none:1

[sarahyk]

Hi @ccbvib, I had a similar issue. Were you able to find a solution or explanation?

[pakiessling]

@ccbvib give this a shot https://github.com/kharchenkolab/Baysor/issues/82#issuecomment-1593566888

[VPetukhov]

@sarahyk , @ccbvib , could you please provide the Baysor version here? It looks like one prior to 0.6.