gersteinlab / mrtadfinder Goto Github PK

$ julia --version
julia version 0.6.1

$ julia run_MrTADFinder.jl /sp4work/Projects/MiniPromoters/SN/Hi-C/HiC-Pro/NcoI/hic_results/hicpro.merged/hic_results/matrix/data/iced/40000/data_40000_iced.matrix ./bins/mm10/bins_file1 ./bins/mm10/bins_file2 res=2.875 21 chr19.bed

WARNING: deprecated syntax "abstract ApproxFit" at /homed/home/oriol/.miniconda2.7/share/julia/site/v0.6/CurveFit/src/CurveFit.jl:47.
Use "abstract type ApproxFit end" instead.

WARNING: deprecated syntax "abstract LeastSquares<:ApproxFit" at /homed/home/oriol/.miniconda2.7/share/julia/site/v0.6/CurveFit/src/CurveFit.jl:50.
Use "abstract type LeastSquares<:ApproxFit end" instead.

WARNING: deprecated syntax "inner constructor LinearFit(...) around /homed/home/oriol/.miniconda2.7/share/julia/site/v0.6/CurveFit/src/linfit.jl:54".
Use "LinearFit{T}(...) where T" instead.

WARNING: deprecated syntax "inner constructor LogFit(...) around /homed/home/oriol/.miniconda2.7/share/julia/site/v0.6/CurveFit/src/linfit.jl:62".
Use "LogFit{T}(...) where T" instead.

WARNING: deprecated syntax "inner constructor PowerFit(...) around /homed/home/oriol/.miniconda2.7/share/julia/site/v0.6/CurveFit/src/linfit.jl:69".
Use "PowerFit{T}(...) where T" instead.

WARNING: deprecated syntax "inner constructor ExpFit(...) around /homed/home/oriol/.miniconda2.7/share/julia/site/v0.6/CurveFit/src/linfit.jl:76".
Use "ExpFit{T}(...) where T" instead.
WARNING: could not import Base.call into CurveFit
reading binning information
reading contact map
WARNING: round(::Type{T}, x::AbstractArray) where T is deprecated, use round.(T, x) instead.
Stacktrace:
 [1] depwarn(::String, ::Symbol) at ./deprecated.jl:70
 [2] round(::Type{Int64}, ::Array{Float64,1}) at ./deprecated.jl:57
 [3] read_generic_WG_contact_map(::String, ::Int64) at /sp4work/Tools/MrTADFinder/MrTADFinder.jl:12
 [4] include_from_node1(::String) at ./loading.jl:576
 [5] include(::String) at ./sysimg.jl:14
 [6] process_options(::Base.JLOptions) at ./client.jl:305
 [7] _start() at ./client.jl:371
while loading /sp4work/Tools/MrTADFinder/run_MrTADFinder.jl, in expression starting on line 49
ERROR: LoadError: ArgumentError: invalid index: 21.0
Stacktrace:
 [1] extract_chr(::SparseMatrixCSC{Float64,Int64}, ::Array{Any,2}, ::Float64) at /sp4work/Tools/MrTADFinder/MrTADFinder.jl:22
 [2] include_from_node1(::String) at ./loading.jl:576
 [3] include(::String) at ./sysimg.jl:14
 [4] process_options(::Base.JLOptions) at ./client.jl:305
 [5] _start() at ./client.jl:371
while loading /sp4work/Tools/MrTADFinder/run_MrTADFinder.jl, in expression starting on line 51