Error in eigen(delta1) : infinite or missing values in x

[dollykc]

Hi Dr. Gosselin,
I used the radiator package to read in my vcf
vcf <- read_vcf(data = "populations.snps.vcf", strata = "Whitefish.strata.tsv", parallel.core = 1L)

I then attempted to use the grur package to perform the identity by missingness analysis and got an error.
ibm.whitefish<-missing_visualization(
vcf,
strata = "Whitefish.strata.tsv",
distance.method = "euclidean",
ind.missing.geno.threshold = c(2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90),
filename = NULL,
parallel.core = 1L,
write.plot = TRUE
)

Here is the output

Default "..." arguments assigned in missing_visualization:
path.folder = NULL

Folder created: missing_visualization_20220713@1009
File written: grur_missing_visualization_data_args_20220713@1009.tsv

Importing data
File written: individuals qc info and stats summary
File written: individuals qc plot

Informations:
Number of populations: 33
Number of individuals: 545
Number of ind/pop:
CclPEND21C = 15
PabBERL20C = 16
PgeBERL19C = 32
PspBERL20C = 16
PwiBGLR2021C = 26
PwiBHNR20C = 14
PwiBIGW0321C = 47
PwiBOIS20C = 18
PwiBRUN21C = 15
PwiCLFR21C = 16
PwiCLWR20C = 16
PwiEFSW14C = 16
PwiGALL20C = 16
PwiHFRK21C = 15
PwiKOTN21C = 14
PwiKOTN21C_1 = 15
PwiLKGC20C = 15
PwiLOGN20C = 16
PwiLSTW20C = 16
PwiMDSN20C = 16
PwiMFWR20C = 16
PwiNFBR21C = 12
PwiNFSR21C = 16
PwiRFLC20C = 16
PwiSFBR21C = 5
PwiSFSN20C = 15
PwiSQPR20C = 11
PwiSTMP20C = 16
PwiTETR20C = 16
PwiTRUC09C = 13
PwiWBSL20C = 16
PwiWLWL20C = 15
PwoYLOR21C = 8

Number of duplicate id: 0
Number of chrom/scaffolds: 1
Number of locus: 182
Number of SNPs: 350

Proportion of missing genotypes (overall): 0.144619
Identity-by-missingness (IBM) analysis using
Principal Coordinate Analysis (PCoA)...
fstcore package v0.9.12
(OpenMP detected, using 12 threads)
Generating Identity by missingness plot
Redundancy analysis...
Error in eigen(delta1) : infinite or missing values in 'x'
In addition: Warning message:
package ‘fstcore’ was built under R version 4.1.3

Computation time, overall: 5 sec

I saw in another error report that someone got the same error when attempting missing_visualization on a genlight object and you suggested it was because one of the pop groups had a size of 1 but that is not the case here. I have 33 populations (strata) and the smallest size is 5.

Here are the results from running session_info()
devtools::session_info()

• Session info ----------------------------------------------------------------------------------------
  setting value
  version R version 4.1.0 (2021-05-18)
  os Windows 10 x64 (build 19044)
  system x86_64, mingw32
  ui RStudio
  language (EN)
  collate English_United States.1252
  ctype English_United States.1252
  tz America/Denver
  date 2022-07-13
  rstudio 2022.02.3+492 Prairie Trillium (desktop)
  pandoc NA

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I've attached my strata file and the first 100 lines of my vcf file as txt files
trunc.populations.snps.vcf.txt
Whitefish.strata.tsv.txt

Thanks for any help,
Kat