error running assignR on converted genepop file

[lplough]

Dear Thierry et al.,

I am getting this error when I run assignR:

Calibrating REF/ALT alleles... Error in if (detect.gt == "GT_VCF_NUC") { : argument is of length zero
when I try to run assignR on a converted genepop file.

Here is my code to load and convert to tidy format:

> packageVersion("assignR") [1] ‘2.0.0’

> packageVersion("radiator") [1] ‘1.1.9’

BC.tidy <- radiator::tidy_genepop(data = "SNP.BC_3.11.21.hwe.bi.recode.gen")

BC.tidy
# A tibble: 2,760,186 x 4
POP_ID INDIVIDUALS MARKERS GT
<fct> <chr> <fct> <chr>
1 1 CED-02 HiC_scaffold_1__9318304_1006119 001001
2 1 CED-03 HiC_scaffold_1__9318304_1006119 001001
3 1 CED-04 HiC_scaffold_1__9318304_1006119 001002
4 1 CED-05 HiC_scaffold_1__9318304_1006119 001001
5 1 CED-06 HiC_scaffold_1__9318304_1006119 001002
6 1 CED-07 HiC_scaffold_1__9318304_1006119 001001
7 1 CED-08 HiC_scaffold_1__9318304_1006119 001002
8 1 CED-08dup HiC_scaffold_1__9318304_1006119 001002
9 1 CED-09 HiC_scaffold_1__9318304_1006119 000000
10 1 CED-10 HiC_scaffold_1__9318304_1006119 002002
… with 2,760,176 more rows

This genpop file was converted from a dDocent-created (free-bayes) VCF file and it loaded fine in genepop or GenoDive etc. has 429 individuals; 6,434 loci; 12,868 alleles;

Then the assignR code:

> test3 <- assigner::assignment_ngs(data = BC.tidy, assignment.analysis = "gsi_sim", marker.number = c(100, 200, "all"), markers.sampling = "ranked", thl = 0.3)

################################################################################
########################## assigner::assignment_ngs ############################
################################################################################
Execution date/time: 20210321@1157
Assignment analysis with gsi_sim
Calibrating REF/ALT alleles...
Error in if (detect.gt == "GT_VCF_NUC") { : argument is of length zero

**Computation time, overall: 2 sec
########################## assignment_ngs completed ############################

Clearly there is a format error with the BC.tidy dataset, but im not sure where Ive gone wrong here. I am sorry if I am missing something obvious, but my understanding was that I could use radiator to convert to a tidy genotype format, and then run assignR on the converted file (the tibble BC.tidy)

UPDATE:
I get the same error on the example dataset from the assignR package (from the tutorial

> data <- data_assigner_sim_01
> test1 <- assigner::assignment_ngs( data = data, assignment.analysis = "gsi_sim", markers.sampling = "ranked", thl = 0.2, iteration.method = 5)
################################################################################
########################## assigner::assignment_ngs ############################
################################################################################
Execution date/time: 20210321@1655
Assignment analysis with gsi_sim
Calibrating REF/ALT alleles...
Error in if (detect.gt == "GT_VCF_NUC") { : argument is of length zero

Computation time, overall: 0 sec
########################## assignment_ngs completed ############################
`

UPDATE- I am able to recreate this same error with the example dataset from the 'getting started' tutorial [here])(http://thierrygosselin.github.io/assigner/articles/get_started.html)

> data <- data_assigner_sim_01
> test1 <- assigner::assignment_ngs( data = data, assignment.analysis = "gsi_sim", markers.sampling = "ranked", thl = 0.2, iteration.method = 5)

################################################################################
########################## assigner::assignment_ngs ############################
################################################################################
Execution date/time: 20210321@1655
Assignment analysis with gsi_sim
Calibrating REF/ALT alleles...
Error in if (detect.gt == "GT_VCF_NUC") { : argument is of length zero

Computation time, overall: 0 sec
########################## assignment_ngs completed ############################

Thanks for any help here!

LP

[esnielsen]

Hi LP,

Did you happen to solve this issue? I am trying with my genepop file at the moment and getting the same error...

Thanks!
Erica

[saat-mics]

Hi,

while reying to estimate fst, I am having the error below:

Calibrating REF/ALT alleles...
Error in purrr::map():
ℹ In index: 1.
Caused by error in dplyr::filter():
ℹ In argument: GT != "000000".
Caused by error:
! object 'GT' not found

Any clue how to solve this?

thanks