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a method to identify TADs in Hi-C data
Hi,
The execution of run_MrTADFinder.jl
on my computer produces multiple warnings an errors. I have tried both julia
versions 0.4.7
and 0.6.1
(I have been unable to find the source code for the version 0.4.3
described in the README.md
file).
Below are the warnings/errors from the 0.6.1
version:
$ 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
FYI, attached is a zip
file with the bin files that I created from the HiC-Pro
file containing the Hi-C fragments (i.e. data_40000_abs.bed
) using the Create_MrTADFinder_Bins.py
script (also attached) .
Any help will be welcome! Thank you in advance!
Hi,
Are there any scripts to generate annotation1 and 2 files ?!
Thank you.
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