Dear dartR Team,
I was hoping to get some advice regarding an error message I receive trying to convert my SNP genlight file into a vcf file using dartR.
I am running under Windows with R version 4.2.1. I have been reading some of the conversations on the Google Group referring to converting genlight file to vcf file, and have tried troubleshooting based on the advice provided in the Google Group. Please see below the code I am using and the error message (in red) I receive:
> gl2vcf(x=gl5,
+ plink_path = getwd(),
+ outfile = "gl5.vcf",
+ outpath = getwd(),
+ snp_pos = "0",
+ snp_chr = "0",
+ chr_format = "character",
+ pos_cM = "0",
+ ID_dad = "0",
+ ID_mom = "0",
+ sex_code = "unknown",
+ phen_value = "0",
+ verbose = NULL)
Starting gl2vcf
Processing genlight object with SNP data
Chromosome information is not present in the slot 'chromosome'. Setting '0' as the name chromosome for all the SNPs.
Starting gl2plink
Processing genlight object with SNP data
Completed: gl2plink
Error in system(..., intern = T) : 'C:/Users/uqlhulse/OneDrive' not found
I look forward to hearing from you and please let me know if I can provide any further information.
Kind regards,
Lyndal
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