failed with GATK output

[lmanchon]

--Hi,

i have tried viva with vcf file generated with GATK suite and it failed with:

julia viva.jl -f GATK.vcf

Welcome to VIVA.

Loading dependency packages:

┌ Warning: ORCA.jl has been deprecated and all savefig functionality
│ has been implemented directly in PlotlyBase itself.
│
│ By implementing in PlotlyBase.jl, the savefig routines are automatically
│ available to PlotlyJS.jl also.
└ @ ORCA C:\Users\admin.julia\packages\ORCA\U5XaN\src\ORCA.jl:8
...

Finished loading packages!

Reading GATK.vcf ...

No filters applied. Large vcf files will take a long time to process and heatmap visualizations will lose resolution at this scale unless viewed in interactive html for zooming.

Loading VCF file into memory for visualization
Selected 21839 variants with no filters applied
ERROR: LoadError: MethodError: no method matching DataFrames.DataFrame(::Type{String}, ::Int64, ::Int64)
Closest candidates are:
DataFrames.DataFrame(::AbstractArray{T,1}, ::AbstractArray{Symbol,1}, ::Integer; makeunique) where T<:Type at C:\Users\admin.julia\packages\DataFrames\nxjiD\src\dataframe\dataframe.jl:374
DataFrames.DataFrame(::AbstractArray{var"#s56",1} where var"#s56"<:Type, ::AbstractArray{var"#s54",1} where var"#s54"<:AbstractString, ::Integer; makeunique) at C:\Users\admin.julia\packages\DataFrames\nxjiD\src\dataframe\dataframe.jl:380
DataFrames.DataFrame(::T; copycols) where T at C:\Users\admin.julia\packages\DataFrames\nxjiD\src\other\tables.jl:48
Stacktrace:
[1] generate_genotype_array(::Array{Any,1}, ::String) at C:\Users\admin.julia\packages\VariantVisualization\WXNGP\src\vcf_utils_complete.jl:664
[2] combined_all_genotype_array_functions(::Array{Any,1}) at C:\Users\admin.julia\packages\VariantVisualization\WXNGP\src\vcf_utils_complete.jl:617
[3] top-level scope at D:\VariantVisualization\viva.jl:408
[4] include(::Function, ::Module, ::String) at .\Base.jl:380
[5] include(::Module, ::String) at .\Base.jl:368
[6] exec_options(::Base.JLOptions) at .\client.jl:296
[7] _start() at .\client.jl:506
in expression starting at D:\VariantVisualization\viva.jl:406

and i don't know what's wrong, any ideas ?

thank you --

[gtollefson]

Hi @lmanchon,

Let's get this solved! Can you try running VIVA using the example VCF file provided within the VariantVisualization.jl/test/test_files/ directory within the package?

As a side note, running VIVA on a set of 21839 variants may be misleading to interpret since this is too many data points to visualize on a standard screen. You may want to consider applying a filter such as a list of variants or regions of interest.

George

[lmanchon]

Again failed with only 422 variants:

julia viva.jl -f GATK.vcf -r chr1:20000-30000000 -s pdf -m genotype,read_depth --avg_dp samples

Welcome to VIVA.

Loading dependency packages:

┌ Warning: ORCA.jl has been deprecated and all savefig functionality
│ has been implemented directly in PlotlyBase itself.
│
│ By implementing in PlotlyBase.jl, the savefig routines are automatically
│ available to PlotlyJS.jl also.
└ @ ORCA C:\Users\ Admin.julia\packages\ORCA\U5XaN\src\ORCA.jl:8
...

Finished loading packages!

Reading GATK.vcf ...

Selected 422 variants within chromosome range: chr1:20000-30000000
ERROR: LoadError: MethodError: no method matching DataFrames.DataFrame(::Type{String}, ::Int64, ::Int64)
Closest candidates are:
DataFrames.DataFrame(::AbstractArray{T,1}, ::AbstractArray{Symbol,1}, ::Integer; makeunique) where T<:Type at C:\Users\ Admin.julia\packages\DataFrames\nxjiD\src\dataframe\dataframe.jl:374
DataFrames.DataFrame(::AbstractArray{var"#s56",1} where var"#s56"<:Type, ::AbstractArray{var"#s54",1} where var"#s54"<:AbstractString, ::Integer; makeunique) at C:\Users\ Admin.julia\packages\DataFrames\nxjiD\src\dataframe\dataframe.jl:380
DataFrames.DataFrame(::T; copycols) where T at C:\Users\ Admin.julia\packages\DataFrames\nxjiD\src\other\tables.jl:48
Stacktrace:
[1] generate_genotype_array(::Array{Any,1}, ::String) at C:\Users\ Admin.julia\packages\VariantVisualization\WXNGP\src\vcf_utils_complete.jl:664
[2] combined_all_genotype_array_functions(::Array{Any,1}) at C:\Users\ Admin.julia\packages\VariantVisualization\WXNGP\src\vcf_utils_complete.jl:617
[3] top-level scope at D:\VariantVisualization\viva.jl:408
[4] include(::Function, ::Module, ::String) at .\Base.jl:380
[5] include(::Module, ::String) at .\Base.jl:368
[6] exec_options(::Base.JLOptions) at .\client.jl:296
[7] _start() at .\client.jl:506
in expression starting at D:\VariantVisualization\viva.jl:406