Stacks vcf to rubias about radiator HOT 4 CLOSED

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######################### radiator::genomic_converter ##########################
################################################################################
Execution date@time: 20220623@1130
Folder created: 12_radiator_genomic_converter_20220623@1130
Function call and arguments stored in: [email protected]
Filters parameters file generated: [email protected]

Importing data: vcf.file

Reading VCF...

Data summary:
    number of samples: 17
    number of markers: 4

Filter monomorphic markers
Number of individuals / strata / chrom / locus / SNP:
    Blacklisted: 0 / 0 / 0 / 1 / 1

Strata with low sample size detected: fig <- FALSE


Filter common markers:
Number of individuals / strata / chrom / locus / SNP:
    Blacklisted: 0 / 0 / 0 / 2 / 2

Generating individual stats...
Generating markers stats...
[==================================================] 100%, completed, 0s
[==================================================] 100%, completed, 0s

Number of chromosome/contig/scaffold: 1
Number of locus: 1
Number of markers: 1
Number of strata: 3
Number of individuals: 17

Number of ind/strata:
Y = 15
S = 1
D = 1

Number of duplicate id: 0
radiator Genomic Data Structure (GDS) file: [email protected]

Genotypes formats generated with 1 SNPs:
    GT_BIN (the dosage of ALT allele: 0, 1, 2 NA): TRUE
    GT_VCF (the genotype coding VCFs: 0/0, 0/1, 1/1, ./.): TRUE
    GT_VCF_NUC (the genotype coding in VCFs, but with nucleotides: A/C, ./.): TRUE
    GT (the genotype coding 'a la genepop': 001002, 001001, 000000): TRUE
LOCUS field empty... adding unique id instead
HQ values are all missing: removing column

Tidy data file written: [email protected]

Computation time, overall: 6 sec

Writing tidy data set:
practising.rad

Preparing data for output

Data is bi-allelic
Generating rubias output
Error in data.table::melt.data.table(data = ., id.vars = cols, measure.vars = measure_vars,  :
  One or more values in 'id.vars' is invalid.
Calls: genomic_converter ... %<>% -> <Anonymous> -> %>% -> <Anonymous> -> <Anonymous>
In addition: Warning messages:
1: Unknown or uninitialised column: `LOCUS`.
2: Unknown or uninitialised column: `VARIANT_ID`.

Computation time, overall: 8 sec
######################### completed genomic_converter ##########################
Execution halted`