detect_duplicate_genomes

[laiajulianamu]

Dear Thierry,

I am running my dataset on a Mac, but for some reason, the process stops at the duplicate genome filter.

Execution date@time: 20240905@1842
File written: [email protected]
Calculating heterozygosity statistics
Generating plots

The greatest value of a picture is when it forces us
to notice what we never expected to see.

John W. Tukey. Exploratory Data Analysis. 1977.

Inspect plots and tables in folder created...
Do you want to exclude individuals based on heterozygosity ? (y/n):
y
Enter the min value for ind.heterozygosity.threshold argument (0 turns off):
0.80
Enter the max value for ind.heterozygosity.threshold argument (1 turns off):
0.98
Filter individual's heterozygosity: 649 individual(s) blacklisted
################################### RESULTS ####################################
Detect mixed genomes: 0.8 0.98
Number of individuals / strata / chrom / locus / SNP:
Before: 649 / 6 / 1 / 21089 / 21089
Blacklisted: 649 / 6 / 0 / 0 / 0
After: 0 / 0 / 1 / 21089 / 21089

Filter monomorphic markers
Number of individuals / strata / chrom / locus / SNP:
Blacklisted: 0 / 0 / 0 / 0 / 0

Computation time, overall: 22 sec
######################## completed detect_mixed_genomes ########################
################################################################################
###################### radiator::detect_duplicate_genomes ######################
################################################################################
Execution date@time: 20240905@1842
Function call and arguments stored in a file
File written: [email protected]
File written: random.seed (791874)
Calculating manhattan distances between individuals...
Error in .InitFile2(cmd = "Identity-By-State (IBS) analysis on genotypes:", :
There is no SNP!
In addition: Warning messages:
1: There was 1 warning in dplyr::mutate().
ℹ In argument: WHITELISTED_MARKERS = purrr::map_int(...).
Caused by warning:
! Using one column matrices in filter() was deprecated in dplyr
1.1.0.
ℹ Please use one dimensional logical vectors instead.
ℹ The deprecated feature was likely used in the radiator package.
Please report the issue at
https://github.com/thierrygosselin/radiator/issues.
This warning is displayed once every 8 hours.
Call lifecycle::last_lifecycle_warnings() to see where this warning
was generated.
2: Removed 2 rows containing missing values or values outside the scale
range (geom_hline()).
3: Removed 2 rows containing missing values or values outside the scale
range (geom_hline()).
4: In min(x, na.rm = TRUE) :
no non-missing arguments to min; returning Inf
5: In max(x, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf

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

Computation time, overall: 567 sec
############################# completed filter_rad #############################

Session info ────────────────────────────────────────────────────────────────
setting value
version R version 4.4.1 (2024-06-14)
os macOS Sonoma 14.6.1
system x86_64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Guayaquil
date 2024-09-05
rstudio 2024.04.2+764 Chocolate Cosmos (desktop)
pandoc NA

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[1] /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library