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[thierrygosselin]

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[iviceron]

Hi!
I am trying to use radiator to convert a VCF file to genepop. This data doesn't have a reference genome. Therefore, it is a the novo_ SNP calling. But, using the radiator, I am having this error:
Error in SeqArray::seqGetData(gdsfile = data, var.name = "$ref") :
The GDS node "$ref" does not exist.

I am assuming the error means that radiator needs a reference genome. If so, how can I solve it? Thanks!

[dawood2014]

I'm having the same issue. Did you ever get a response that helped solve the issue?

[thierrygosselin]

reference genome not required
try again with the latest release, some bug introduced in recent release were corrected

if you're still having a problem, follow guidelines to open an issue in order to make the error reproducible on my end.

[Sapicq]

Hello,

I'am having also the same kind of issue... I am trying to use the fonction tidy_genomic_data in radiator to convert a VCF file to a tidy.vcf format. I had already successfully converted the same vcf file with this function in a previous version of radiator (v1.1.5).

Installation
Windows Server 2012 R2 Standard
R version 4.2.1
radiator_1.2.2
SeqArray_1.36.3

Code

library(radiator)
tidy.vcf <- tidy_genomic_data(data = "HapMap_MD_S80I25_MAF0.01_He0.6_hwe_SnpD_IndD_1SNP_LD_1156_Assigner_20200501.vcf", strata = "Pop_assigner_19g_updtae_20220915.txt")
################################################################################
######################### radiator::tidy_genomic_data ##########################
################################################################################
Execution date@time: 20220922@1858
Folder created: -8_radiator_tidy_genomic_20220922@1858
Function call and arguments stored in: [email protected]
Analyzing strata file
Number of strata: 19
Number of individuals: 1156
Importing and tidying the VCF...
Execution date@time: 20220922@1858

Reading VCF...

Data summary:
number of samples: 1156
number of markers: 2340
Error in SeqArray::seqGetData(gdsfile = data, var.name = "$ref") :
The GDS node "$ref" does not exist.

Computation time, overall: 18 sec
############################## completed tidy_vcf ##############################

Computation time, overall: 18 sec
######################### completed tidy_genomic_data ##########################

Interestingly when I used a subset of my dataset (only 116 SNPs with 1156 individuals), I have another message error:

tidy.vcf <- tidy_genomic_data(data = "/Users/Admin/Documents/HapMap_1156_subset_Assigner_20220922.vcf", strata = "/Users/Admin/Documents/Pop_assigner_19g_updtae_20220915.txt")
################################################################################
######################### radiator::tidy_genomic_data ##########################
################################################################################
Execution date@time: 20220922@2008
Folder created: 00_radiator_tidy_genomic_20220922@2008
Function call and arguments stored in: [email protected]
Analyzing strata file
Number of strata: 19
Number of individuals: 1156
Importing and tidying the VCF...
Execution date@time: 20220922@2008

Reading VCF...

Data summary:
number of samples: 1156
number of markers: 116

Filter monomorphic markers
Number of individuals / strata / chrom / locus / SNP:
Blacklisted: 0 / 0 / 0 / 0 / 0
Error in SeqArray::seqMissing(gdsfile = x, per.variant = TRUE, .progress = FALSE, :
unused argument (.progress = FALSE)
In addition: Warning message:
In as.POSIXlt.POSIXct(x, tz) : unable to identify current timezone 'C':
please set environment variable 'TZ'

Computation time, overall: 2 sec
############################## completed tidy_vcf ##############################

Computation time, overall: 2 sec
######################### completed tidy_genomic_data ##########################

Fichiers
file.zip

Thanks for the help !

[tafarakundai]

Hello,

I had radiator package before and it was working, but when I got a new computer I am failing to install radiator. The error is related to authorisation token issue, I tried generating one and it is not working.
Using GitHub PAT from the git credential store.
Error: Failed to install 'unknown package' from GitHub:
HTTP error 401.
Bad credentials

Rate limit remaining: 47/60
Rate limit reset at: 2024-03-21 20:13:19 UTC

May you kindly help with this issue