Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error in genomic_converter while converting VCF to STRUCTURE format #190

Open
Pigrenok opened this issue Jun 22, 2024 · 0 comments
Open

Comments

@Pigrenok
Copy link

I am trying to run genomic_converter from VCF file to STRUCTURE format, but get a strange error that the default parameter of a radiator_parameter` function is not acceptable.

Here is the full run (including testing VCF file with detect_genomic_format and strata file with read_strata.

> library(radiator)
> radiator::detect_genomic_format(data = "test.vcf")
[1] "vcf.file"
> strata = radiator::read_strata("strata_breed_3_far.tsv")
> res = genomic_converter(data = 'test.vcf', strata = "strata_breed_3_far.tsv", output = c("structure"))                                                                    
################################################################################
######################### radiator::genomic_converter ##########################
################################################################################
Execution date@time: 20240623@0240
Folder created: 08_radiator_genomic_converter_20240623@0240
Function call and arguments stored in: [email protected]
Filters parameters file generated: [email protected]
v Reading VCF [1s]                                                                                       
i Importing data: vcf.file
Cleaning VCF
LOCUS field empty... adding unique id instead
Filtering markers based on VCF FILTER column
Error in `radiator_parameters()`:
! parameter.obj = NULL not accepted
Run `rlang::last_trace()` to see where the error occurred.

Computation time, overall: 5 sec

Computation time, overall: 5 sec
######################### completed genomic_converter ##########################
x Importing data: vcf.file [5.3s]

Here is the test data that I use with here.
test.tar.gz

Any ideas what can be done with it?

Thank you very much in advance.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant