gtollefson
commented
3 years ago @coraolpe Hi Cora,
Thank you for bringing this issue up. I'm sorry for my delayed response. Do you still need help with this? I think the issue may be that the output directory parameter does not expect a '/' character at the end of the directory name. Have you tried running it with the following command instead?
Julia viva -f 20190219_Gli1_5d_A03_Recalibratedhaplo_called.vcf -o viva_output -s pdf
Let me know how it goes and if you have any other issues!
George
Hi,
This is the first time I'm trying to use VIVA. I followed GATK best practices to generate a vcf file that I want to visualise. I am using a cluster.
I ran: Julia viva -f 20190219_Gli1_5d_A03_Recalibratedhaplo_called.vcf -o viva_output/ -s pdf
And I got this error: ERROR: LoadError: MethodError: PlotlyBase.savefig(::PlotlyJS.SyncPlot, ::String) is ambiguous. Candidates: savefig(p::PlotlyJS.SyncPlot, a...) in PlotlyJS at /home/cluster/colpe/.julia/packages/PlotlyJS/AhkM5/src/savefig_orca.jl:1 savefig(p::Union{SyncPlot, Plot}, fn::AbstractString, args...) in PlotlyJS at /home/cluster/colpe/.julia/packages/PlotlyJS/AhkM5/src/PlotlyJS.jl:49 Possible fix, define savefig(::PlotlyJS.SyncPlot, ::AbstractString, ::Vararg{Any,N} where N) Stacktrace: [1] save_graphic(::PlotlyJS.SyncPlot, ::String, ::String, ::String, ::Bool) at /home/cluster/colpe/.julia/packages/VariantVisualization/1yoNl/src/vcf_utils_complete.jl:1479 [2] top-level scope at /home/cluster/colpe/.julia/packages/VariantVisualization/1yoNl/viva:479 [3] include at ./boot.jl:326 [inlined] [4] include_relative(::Module, ::String) at ./loading.jl:1038 [5] include(::Module, ::String) at ./sysimg.jl:29 [6] exec_options(::Base.JLOptions) at ./client.jl:267 [7] _start() at ./client.jl:436 in expression starting at /home/cluster/colpe/.julia/packages/VariantVisualization/1yoNl/viva:407
Not sure what to do now... I would greatly appreciate some help. Kind regards Cora