ERROR: LoadError: ArgumentError

[Asoorni]

Hi,

I get the following error with every VCF I try to analyse but it works well will test file!

ERROR: LoadError: ArgumentError: invalid base 10 digit 'S' in "Super_scaffold_232" Stacktrace: [1] tryparse_internal(::Type{Int64}, ::String, ::Int64, ::Int64, ::Int64, ::Bool) at ./parse.jl:132 [2] #parse#347(::Nothing, ::typeof(parse), ::Type{Int64}, ::String) at ./parse.jl:238 [3] parse at ./parse.jl:238 [inlined] [4] #23 at ./none:0 [inlined] [5] iterate at ./generator.jl:47 [inlined] [6] collect_to! at ./array.jl:667 [inlined] [7] collect_to_with_first!(::Array{Int64,2}, ::Int64, ::Base.Generator{Array{String,2},VariantVisualization.var"#23#25"}, ::Int64) at ./array.jl:646 [8] collect(::Base.Generator{Array{String,2},VariantVisualization.var"#23#25"}) at ./array.jl:627 [9] sort_genotype_array(::Array{String,2}) at /Users/DragonsTooth/.julia/packages/VariantVisualization/1yoNl/src/vcf_utils_complete.jl:688 [10] combined_all_genotype_array_functions(::Array{Any,1}) at /Users/DragonsTooth/.julia/packages/VariantVisualization/1yoNl/src/vcf_utils_complete.jl:620 [11] top-level scope at /usr/local/bin/viva:409 [12] include at ./boot.jl:328 [inlined] [13] include_relative(::Module, ::String) at ./loading.jl:1105 [14] include(::Module, ::String) at ./Base.jl:31 [15] exec_options(::Base.JLOptions) at ./client.jl:287 [16] _start() at ./client.jl:460 in expression starting at /usr/local/bin/viva:407

So I am pretty sure there is a problem in my VCF file but I checked every think and couldn't find any problem!

This is a part of this scaffold in my VCF file!

Super_scaffold_232 69631 . C T 38.24 PASS AC=2;AF=1.00;AN=2;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=19.12;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ./.:15,0:15:.:0,0,0 Super_scaffold_232 348623 . T C 304.64 PASS AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.83;SOR=1.863 GT:AD:DP:GQ:PL 1/1:0,8:8:24:317,24,0 ./.:0,0:0:.:0,0,0 Super_scaffold_232 348639 . C G 279.51 PASS AC=2;AF=1.00;AN=2;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.21;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,7:7:21:292,21,0 ./.:0,0:0:.:0,0,0 Super_scaffold_232 348679 . G C 321.64 PASS AC=2;AF=1.00;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.02;SOR=1.863 GT:AD:DP:GQ:PL 1/1:0,8:8:24:334,24,0 ./.:0,0:0:.:0,0,0

Am I doing something wrong?

[gtollefson]

Hi @Asoorni ,

Thanks for posting the stacktrace and the VCF snippet - that is very helpful.

You are receiving this error because VIVA only recognizes human chromosomes 1-22 and X,Y,M (for mitochondrial). The scaffold name Super_scaffold_232 isn't recognized by the program which tries to sort variants by chromosomal order.

We are still developing a new version that is able to analyze VCF files for all genomes/sets of chromosome names including custom assemblies with custom scaffold names. I'm sorry we're not able to accommodate your variant analysis goal with our current version. I'll try to remember to reply to this thread again to alert you when this feature is supported!

[fredjaya]

I stumbled across an identical error with `ERROR: LoadError: ArgumentError: invalid base 10 digit 'N' in "NC_037638.1".

Great to see that the issue has been raised and newer versions will account for custom/non-human assemblies, looking forward to it! 😊

[gtollefson]

@fredjaya I'll try to tag you in this thread once we develop this feature! Our development focus is not on VIVA at the moment, so it may be a few months before non-human and custom assemblies are supported. Thank you for understanding!

[leorippel]

Hi,

Having the same problem

"ERROR: LoadError: ArgumentError: invalid base 10 digit 'd' in "disjointig_10"

Looking forward to Viva accept other than human vcf.