Error in loading VCF file provide by Gubbins

[Nilad]

I try to use/discover your package with a classic gubbins vcf output.

Command

sudo viva -f gubbins.summary_of_snp_distribution.vcf

Prompt

Welcome to VIVA.

Loading dependency packages:

/MYHOME/.julia/conda/3/envs/_ORCA_jl_/lib/orca_app/orca: error while loading shared libraries: libgconf-2.so.4: cannot open shared object file: No such file or directory
...

Finished loading packages!

Reading gubbins.summary_of_snp_distribution.vcf ...

ERROR: LoadError: GeneticVariation.VCF.Reader file format error on line 4
Stacktrace:
 [1] error(::String, ::Int64) at ./error.jl:42
 [2] _readheader!(::GeneticVariation.VCF.Reader, ::BioCore.Ragel.State{BufferedStreams.BufferedInputStream{IOStream}}) at /MYHOME/.julia/packages/BioCore/YBJvb/src/ReaderHelper.jl:106
 [3] readheader!(::GeneticVariation.VCF.Reader) at /MYHOME/.julia/packages/BioCore/YBJvb/src/ReaderHelper.jl:80
 [4] Reader at /MYHOME/.julia/packages/GeneticVariation/r8DAL/src/vcf/reader.jl:15 [inlined]
 [5] GeneticVariation.VCF.Reader(::IOStream) at /MYHOME/.julia/packages/GeneticVariation/r8DAL/src/vcf/reader.jl:28
 [6] top-level scope at /usr/local/bin/viva:130
 [7] include at ./boot.jl:328 [inlined]
 [8] include_relative(::Module, ::String) at ./loading.jl:1105
 [9] include(::Module, ::String) at ./Base.jl:31
 [10] exec_options(::Base.JLOptions) at ./client.jl:287
 [11] _start() at ./client.jl:460
in expression starting at /usr/local/bin/viva:130

[gtollefson]

@Nilad Thank you for your question. It looks like VIVA has a problem with the way the VCF header is formatted. Can you send me line 4 of the VCF file so I can help troubleshoot?

Can you also tell me the version of Julia you are running and what OS you are using?

Thanks! George

[Nilad]

##fileformat=VCFv4.2
##contig=<ID=1,length=2045255>
##FORMAT=<ID=AB,Number=1,Type=String,Description="Alt Base">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  X1  X2                                  
1   628 .   G   N,A .   .   .   AB  G   G