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View Code? Open in Web Editor NEWPopulation assignment analysis using R
Home Page: http://thierrygosselin.github.io/assigner
License: GNU General Public License v3.0
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Syntax error
Hi, I'm really excited about using assigner, but I keep getting an error when trying to run it. It seems to create 'fst.ranked_.tsv' and 'assignment_data_iteration__markers_10_no_imputation.txt" files, but then throws this error. I've run the file in genepop, so I'm relatively sure that it is formatted properly. I've also gotten a different genepop file to run through assigner without problems. Any insight on what might be holding up this file? Below is an example input file.
Thanks,
Dan Drinan
library(assigner)
library(reshape2)
library(ggplot2)
library(stringr)
library(stringi)
library(plyr)
library(dplyr) # load this package after plyr to work properly
library(tidyr)
library(readr)
library(adegenet)
library(randomForestSRC)
library(doParallel)
library(foreach)
library(purrr)
library(utils)
library(iterators)
library(stats)
library(stackr)
my_data <-read.genepop("test.gen", ncode = 2) #save your genepop file as a genind object named mydata
Converting data from a Genepop .gen file to a genind object...
File description: #Title: removed loci with 3 alleles
...done.
mytidydata <- tidy_genomic_data(data = my_data)
#######################################################################
###################### stackr::tidy_genomic_data ######################
#######################################################################
Tidying the genind object ...
Scanning for number of alleles per marker...
Data is biallellic
Generating vcf-style coding
Erasing genotype: no
Using markers common in all populations:
Number of markers before = 50
Number of markers removed = 0
Number of markers after (common between populations) = 50
Removing monomorphic markers: yes
Scanning for monomorphic markers...
Number of markers before = 50
Number of monomorphic markers removed = 10
Number of markers after = 40
############################### RESULTS ###############################
Tidy data in your global environment
Data format: tbl_df
Biallelic data
Number of common markers: 40
Number of chromosome/contig/scaffold: no chromosome info
Number of individuals: 276
Number of populations: 8
Computation time: 0 sec
############################## completed ##############################
my_assignment <- assignment_ngs(mytidydata, #specify that your data file
assignment.analysis = "gsi_sim", # specify that the analysis happens in gsi_sim
sampling.method = "ranked", #specify that the assignment should happen using markers with high FST
thl = 10, # specify that you want to use the training-holdout-leave one out assignment method. thl = 1, 1 individual sample is used as holdout. This individual is not participating in the markers ranking.
iteration.method = 10,
subsample = NULL,
#iteration.subsample = 10,
common.markers = TRUE,
marker.number = 10,
verbose = TRUE,
folder = NULL,
keep.gsi.files = TRUE,
random.seed = NULL,
parallel.core = parallel::detectCores() - 1)
#######################################################################
###################### assigner::assignment_ngs #######################
#######################################################################
Assignment analysis with gsi_sim
Map-independent imputations: no
Folder: /home/dan/Dropbox (MERLAB)/Pacific_cod/cod_kristen/assigner/assignment_analysis_method_ranked_no_imputations_20170705@1527/
Scanning for monomorphic markers...
Number of markers before = 40
Number of monomorphic markers removed = 0
Subsampling: not selected
Conducting Assignment analysis with ranked markers
Using thl method, ranking Fst with training samples...
Holdout samples saved in your folder
Starting parallel computations for the assignment analysis: ranked markers
For progress: monitor activity in the folder...
| | 0%, ETA NA
sh: 1: Syntax error: "(" unexpected
sh: 1: Syntax error: "(" unexpected
sh: 1: Syntax error: "(" unexpected
sh: 1: Syntax error: "(" unexpected
sh: 1: Syntax error: "(" unexpected
sh: 1: Syntax error: "(" unexpected
sh: 1: Syntax error: "(" unexpected
sh: 1: Syntax error: "(" unexpected
sh: 1: Syntax error: "(" unexpected
sh: 1: Syntax error: "(" unexpected
Compiling results
Error in bind_rows_(x, .id) : 'getCharCE' must be called on a CHARSXP
In addition: Warning message:
In .assigner_parallel(X = iterations.list, FUN = assignment_ranking, :
scheduled cores encountered errors in user code
Function assignment_mixture no longer available in v0.5.7?
Hi!
I used assigner to to perform assignments on a group of baseline samples a month ago. Now I get a new set of samples of unknown origins, and I would like to assign this batch to the baseline samples. Previously we have the function assignment_mixture to perform such kind of tasks, but it seems this function was disabled in the latest assigner v0.5.7?
Thanks a lot,
Peiwen
Issues using tidy_vcf function
Describe the bug
I have tried to calculate Fst on a vcf file obtained through a "home-made" ddocent pipeline.
To do so, I first need to import and transform the vcf in a tidy data frame in R.
I used the following command:
data <- radiator::tidy_vcf(
data = "Amp_a_TotalSNPs_filtred_without_contigs.haplo.vcf",
strata = "pop_map_Amp_a.txt",
gt = TRUE,
tidy.check = FALSE# skip the test for number of markers, otherwise it ask during tidying...
)
It seems that it recognised my pop strata and the number of individuals in the VCF.
Yet I am getting the following error message at the end (see screenshot)
Thanks in advance for your help,
Laura
Heat map error
Hi Thierry,
I've got the following error when trying to make a heatmap with the assigner 0.5.7:
> heat.fst <- heatmap_fst(fst.ci$pairwise.fst.full.matrix, fst.ci$pairwise.fst.ci.matrix, n.s = TRUE,
+ digits = 3, color.low = "white", color.mid = "grey",
+ color.high = "black", text.size = 4, plot.size = 40,
+ path.folder = NULL, filename = NULL)
Error: Can't join on `x$POP1` x `y$POP1` because of incompatible types.
ℹ `x$POP1` is of type <ordered<09208>>>.
ℹ `y$POP1` is of type <ordered<58a21>>>.
Run `rlang::last_error()` to see where the error occurred.
Details:
> rlang::last_error()
<error/rlang_error>
Can't join on `x$POP1` x `y$POP1` because of incompatible types.
ℹ `x$POP1` is of type <ordered<2bfb4>>>.
ℹ `y$POP1` is of type <ordered<4d8de>>>.
Backtrace:
1. assigner::fst_WC84(...)
2. assigner::heatmap_fst(...)
5. [ `%>%`(...) ] with 7 more calls
14. dplyr:::left_join.data.frame(., ns, by = c("POP1", "POP2"))
15. dplyr:::join_mutate(...)
16. dplyr:::join_rows(x_key, y_key, type = type, na_equal = na_equal)
17. base::tryCatch(...)
18. base:::tryCatchList(expr, classes, parentenv, handlers)
19. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
20. value[[3L]](cond)
Run `rlang::last_trace()` to see the full context.
Warning message:
Internal error: Trace data is not square.
> rlang::last_trace()
<error/rlang_error>
Can't join on `x$POP1` x `y$POP1` because of incompatible types.
ℹ `x$POP1` is of type <ordered<2bfb4>>>.
ℹ `y$POP1` is of type <ordered<4d8de>>>.
Backtrace:
█
1. └─assigner::fst_WC84(...)
2. └─assigner::heatmap_fst(...)
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. └─`%>%`(...)
6. ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
7. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
8. └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
9. └─assigner:::`_fseq`(`_lhs`)
10. └─magrittr::freduce(value, `_function_list`)
11. ├─base::withVisible(function_list[[k]](value))
12. └─function_list[[k]](value)
13. ├─dplyr::left_join(., ns, by = c("POP1", "POP2"))
14. └─dplyr:::left_join.data.frame(., ns, by = c("POP1", "POP2"))
15. └─dplyr:::join_mutate(...)
16. └─dplyr:::join_rows(x_key, y_key, type = type, na_equal = na_equal)
17. └─base::tryCatch(...)
18. └─base:::tryCatchList(expr, classes, parentenv, handlers)
19. └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
20. └─value[[3L]](cond)
> devtools::session_info()
─ Session info
────────
setting value
version R version 4.0.2 (2020-06-22)
os Ubuntu 20.04.1 LTS
system x86_64, linux-gnu
─ Packages
───────────────────────────────────────────────────────
package * version date lib source
ade4 1.7-15 2020-02-13 [1] CRAN (R 4.0.2)
adegenet 2.1.3 2020-05-10 [1] CRAN (R 4.0.2)
ape 5.4-1 2020-08-13 [1] CRAN (R 4.0.2)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
assigner * 0.5.7 2020-09-11 [1] Github (thierrygosselin/assigner@da61eb8)
backports 1.1.9 2020-08-24 [1] CRAN (R 4.0.2)
Biobase 2.48.0 2020-04-27 [1] Bioconductor
BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.2)
Biostrings 2.56.0 2020-04-27 [1] Bioconductor
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.2)
boot 1.3-25 2020-04-26 [4] CRAN (R 4.0.0)
broom 0.7.0 2020-07-09 [1] CRAN (R 4.0.2)
callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.2)
class 7.3-17 2020-04-26 [4] CRAN (R 4.0.0)
classInt 0.4-3 2020-04-07 [1] CRAN (R 4.0.2)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2)
cluster 2.1.0 2019-06-19 [4] CRAN (R 4.0.0)
coda 0.19-3 2019-07-05 [1] CRAN (R 4.0.2)
codetools 0.2-16 2018-12-24 [4] CRAN (R 4.0.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.2)
data.table 1.13.0 2020-07-24 [1] CRAN (R 4.0.2)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2)
deldir 0.1-28 2020-07-15 [1] CRAN (R 4.0.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
devtools * 2.3.1 2020-07-21 [1] CRAN (R 4.0.2)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2)
dplyr 1.0.2 2020-08-18 [1] CRAN (R 4.0.2)
e1071 1.7-3 2019-11-26 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
expm 0.999-5 2020-07-20 [1] CRAN (R 4.0.2)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.2)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
fst 0.9.4 2020-08-27 [1] CRAN (R 4.0.2)
gdata 2.18.0 2017-06-06 [1] CRAN (R 4.0.2)
gdsfmt 1.24.1 2020-06-16 [1] Bioconductor
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2)
GenomeInfoDb 1.24.2 2020-06-15 [1] Bioconductor
GenomeInfoDbData 1.2.3 2020-09-11 [1] Bioconductor
GenomicRanges 1.40.0 2020-04-27 [1] Bioconductor
ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
gmodels 2.18.1 2018-06-25 [1] CRAN (R 4.0.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
gtools 3.8.2 2020-03-31 [1] CRAN (R 4.0.2)
GWASExactHW 1.01 2013-01-05 [1] CRAN (R 4.0.2)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.2)
htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2)
igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.2)
IRanges 2.22.2 2020-05-21 [1] Bioconductor
KernSmooth 2.23-17 2020-04-26 [4] CRAN (R 4.0.0)
labeling 0.3 2014-08-23 [1] CRAN (R 4.0.2)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2)
lattice 0.20-41 2020-04-02 [4] CRAN (R 4.0.0)
LearnBayes 2.15.1 2018-03-18 [1] CRAN (R 4.0.2)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)
logistf 1.23.1 2020-09-04 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)
MASS 7.3-53 2020-09-09 [4] CRAN (R 4.0.2)
Matrix 1.2-18 2019-11-27 [4] CRAN (R 4.0.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2)
mgcv 1.8-33 2020-08-27 [4] CRAN (R 4.0.2)
mice 3.11.0 2020-08-05 [1] CRAN (R 4.0.2)
mime 0.9 2020-02-04 [1] CRAN (R 4.0.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
nlme 3.1-149 2020-08-23 [4] CRAN (R 4.0.2)
pbmcapply 1.5.0 2019-07-10 [1] CRAN (R 4.0.2)
permute 0.9-5 2019-03-12 [1] CRAN (R 4.0.2)
pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)
promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2)
ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
radiator * 1.1.7 2020-09-11 [1] Github (thierrygosselin/radiator@ff31083)
raster 3.3-13 2020-07-17 [1] CRAN (R 4.0.2)
Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.2)
readr 1.3.1 2018-12-21 [1] CRAN (R 4.0.2)
remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.2)
rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2)
S4Vectors 0.26.1 2020-05-16 [1] Bioconductor
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
SeqArray 1.28.1 2020-06-16 [1] Bioconductor
seqinr 3.6-1 2019-09-07 [1] CRAN (R 4.0.2)
SeqVarTools 1.26.0 2020-04-27 [1] Bioconductor
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
sf 0.9-5 2020-07-14 [1] CRAN (R 4.0.2)
shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2)
sp 1.4-2 2020-05-20 [1] CRAN (R 4.0.2)
spData 0.3.8 2020-07-03 [1] CRAN (R 4.0.2)
spdep 1.1-5 2020-06-29 [1] CRAN (R 4.0.2)
stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2)
tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)
tidyr 1.1.2 2020-08-27 [1] CRAN (R 4.0.2)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2)
units 0.6-7 2020-06-13 [1] CRAN (R 4.0.2)
UpSetR 1.4.0 2019-05-22 [1] CRAN (R 4.0.2)
usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.2)
utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.2)
vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2)
vegan 2.5-6 2019-09-01 [1] CRAN (R 4.0.2)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.2)
XVector 0.28.0 2020-04-27 [1] Bioconductor
zlibbioc 1.34.0 2020-04-27 [1] Bioconductor
dependencies
Hi, I'm trying to install assigner on a machine running Windows 10 and R 3.3.0. I get an error that I need to update package 'pmbcapply' to version >= 1.3. My understanding is that this package only goes up to 1.0 for Windows. Do you have a work around for this (or am I wrong)? Thanks for any help you can provide.
Error in bind_rows_(x, .id)
Hi there,
I am new to assignment analysis and found your package straight forward and somewhat easy to use. I have a panel of SNP information in genepop format and everytime I run the assignment_ngs() function I get the following error:
assignment12 <- assignment_ngs(tidy12, assignment.analysis = "gsi_sim", sampling.method = "ranked", thl = 0.5, snp.ld = NULL, iteration.subsample = 10, common.markers = FALSE, blacklist.id = NULL, subsample = 5, filename = "12SNP-Panel-run.txt", keep.gsi.files = FALSE, pop.levels = NULL, random.seed = 100, folder = "Vivax12")
#######################################################################
###################### assigner::assignment_ngs #######################
#######################################################################
Assignment analysis with gsi_sim
Folder: /Users/aford29/Downloads/Vivax12/
Scanning for monomorphic markers...
Number of markers before/blacklisted/after: 12/0/12
Tidy genomic data:
Number of markers: 12
Number of chromosome/contig/scaffold: no chromosome info
Number of individuals: 294
Number of populations: 5
Subsampling: selected
Analyzing subsample: 1
Conducting Assignment analysis with ranked markers
Using thl method, ranking Fst with training samples...
Holdout samples saved in your folder
Starting parallel computations for the assignment analysis: ranked markers
For progress: monitor activity in the folder...
| | 0%, ETA NA
Compiling results
Error in bind_rows_(x, .id) : Argument 1 must have names
In addition: Warning messages:
1: In dir.create(file.path(directory)) :
'/Users/aford29/Downloads/Vivax12' already exists
2: In .assigner_parallel(X = iterations.list, FUN = assignment_ranking, :
scheduled cores encountered errors in user code
The warnings at the end just started happening, but the "Error in bind_rows_(x, .id):" has been occurring for every file that I've tried. I've also tried other files and sample files with the same error. If it helps I attached a sample of the file that I am working with
I'm not sure if it is the file that is giving me the trouble (maybe formatting errors) but I compared them with others that seemed to work and formatting wise everything seemed pretty much the same. I thought maybe using the strata function would work, but the function individuals2strata didn't work out as I may have to make one from scratch. Sorry if it seems my question/issue is all over the place; I'm pretty new to the field.
Any help you can provide would be much appreciated.
Reading VCF... Error in SeqArray::seqOpen(gds.fn = data.safe$result, readonly = FALSE) : is.character(gds.fn) is not TRUE
Hi,
when using assigner
mf<-radiator::genomic_converter(data="/gpfs/gpfs0/genomdata/Ecogenome/periwinkle/stacks/populations/s1_50%_50%_217ind_fullfiltered.recode.vcf", strata="/gpfs/gpfs0/genomdata/Ecogenome/periwinkle/stacks/populations/s1_pop") %>%dplyr::glimpse()
I get the following error:
################################################################################
######################### radiator::genomic_converter ##########################
################################################################################
Execution date@time: 20230223@1627
Folder created: -277260_radiator_genomic_converter_20230223@1627
Function call and arguments stored in: [email protected]
Filters parameters file generated: [email protected]
Reading VCF...
Error in SeqArray::seqOpen(gds.fn = data.safe$result, readonly = FALSE) :
is.character(gds.fn) is not TRUE
Computation time, overall: 6 sec
Computation time, overall: 14 sec
######################### completed genomic_converter ##########################
✖ Importing data: vcf.file [6.7s]
could you please help me with this?
Error in cbind_all(x)
Hi Thierry,
I'm running assigner to test assignment success between two large groups of samples and I found a weird error message occurring in the marker.number option.
What is the error ?: when I define a marker list > 3 elements (last element corresponding to all markers) it crash.
VCF file detailed
*version 4.2
*from stacks v.1.48
*N individuals = 4066
*N snps = 7151
R Script example
library(assigner)
message("perform assignment...")
#Two Regions - north & south
assign1 <- assigner::assignment_ngs(
data = "batch_3_p70_x9_H0.6_y9_no_singletons_4066indv.vcf",
marker.number = c(100, 500, 1000, 2500, 6000, "all"),
sampling.method = "ranked",
thl = 0.5, iteration.method = 10,
assignment.analysis = "gsi_sim",
subsample = 1000,
iteration.subsample=5,
strata = "strata_NS.txt",
parallel.core = 5,
#common.markers = FALSE,
#snp.ld=FALSE,
folder = "THL_0.5_iteration_10_regions-sampling_NOR_SOU_test")
Shell error:
radiator is working on file ...
VCF is biallelic
updating markers metadata and stats
[====...] 100%
Error in cbind_all(x) : Argument 3 must be length 7151, not 63
So 7151 correspond to the nSNPs number however I don't understand the 63
Bioinformatic resources:
Unix server calcul (SLURM)
CPU allowed from 2 to 8 (same error)
RAM allowed 20G
R v.3.5.1
Something weird is that when I fix the marker.number to only 3 element as c(100,1000,7151) it works...
Do you have an idea about this ? I think that the pb is located in radiator vcf importation.
Best,
Yann.
error running assignR on converted genepop file
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
assigner::assignment_ngs() - Error in dplyr::bind_rows(.) : Argument 1 must have names.
Dear Thierry,
Description of the bug
assigner::assignment_ngs does not work with the dataset data_assigner_sim_01 included in assigner - suspecting it is a dplyr issue. I tried dplyr v1.0.0 and the latest v1.0.10 without sucess.
I used the dataset included in assigner after having problems with my own dataset. I wanted to know if it was a problem with the formatting of my data (also dplyr related issue) or if it was the function.
To reproduce
library(assigner)
data<- data_assigner_sim_01
test1 <- assigner::assignment_ngs(
data = data,
assignment.analysis = "gsi_sim",
markers.sampling = "ranked",
thl = 0.2,
iteration.method = 5
)
error message
################################################################################
########################## assigner::assignment_ngs ############################
################################################################################
Execution date/time: 20221206@1917
Assignment analysis with gsi_sim
Subsampling: not selected
Conducting Assignment analysis using Training, Holdout, Leave-one-out
Using training samples to rank markers based on Fst
Holdout samples saved in your folder
Starting parallel computations, for progress monitor activity in folder...
Ranking markers based on Fst
Removing holdout individuals
Fst computation...
Error in dplyr::bind_rows(.) : Argument 1 must have names.
Computation time, overall: 6 sec
########################## assignment_ngs completed ############################
- output of
devtools::session_info()
Session info ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 4.2.1 (2022-06-23 ucrt)
os Windows Server 2012 R2 x64 (build 9600)
system x86_64, mingw32
ui Rgui
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz unknown
date 2022-12-06
pandoc NA
- Packages -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
package * version date (UTC) lib source
ade4 1.7-20 2022-11-01 [1] CRAN (R 4.2.2)
adegenet 2.1.8 2022-10-02 [1] CRAN (R 4.2.2)
ape 5.6-2 2022-03-02 [1] CRAN (R 4.2.1)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.1)
assigner * 0.5.8 2022-09-15 [1] Github (thierrygosselin/assigner@d39a692)
bit 4.0.4 2020-08-04 [1] CRAN (R 4.2.1)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.1)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.1)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.2)
carrier 0.1.0 2018-10-16 [1] CRAN (R 4.2.1)
cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.2)
cluster 2.1.4 2022-08-22 [1] CRAN (R 4.2.1)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.2.1)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.1)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.2)
curl 4.3.3 2022-10-06 [1] CRAN (R 4.2.2)
data.table 1.14.4 2022-10-17 [1] CRAN (R 4.2.2)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.1)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.2.2)
digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.2)
dplyr * 1.0.10 2022-09-01 [1] CRAN (R 4.2.2)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.1)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.1)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.1)
furrr 0.3.1 2022-08-15 [1] CRAN (R 4.2.1)
future 1.29.0 2022-11-06 [1] CRAN (R 4.2.2)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.1)
ggplot2 3.4.0 2022-11-04 [1] CRAN (R 4.2.2)
globals 0.16.2 2022-11-21 [1] CRAN (R 4.2.2)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.1)
hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.1)
htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.1)
httpuv 1.6.6 2022-09-08 [1] CRAN (R 4.2.1)
igraph 1.3.5 2022-09-22 [1] CRAN (R 4.2.2)
later 1.3.0 2021-08-18 [1] CRAN (R 4.2.1)
lattice 0.20-45 2021-09-22 [2] CRAN (R 4.2.1)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.2)
listenv 0.8.0 2019-12-05 [1] CRAN (R 4.2.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
MASS 7.3-58.1 2022-08-03 [1] CRAN (R 4.2.1)
Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.2)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.1)
mgcv 1.8-40 2022-03-29 [2] CRAN (R 4.2.1)
mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.1)
nlme 3.1-160 2022-10-10 [1] CRAN (R 4.2.2)
parallelly 1.32.1 2022-07-21 [1] CRAN (R 4.2.1)
permute 0.9-7 2022-01-27 [1] CRAN (R 4.2.1)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.1)
pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.2)
plyr 1.8.8 2022-11-11 [1] CRAN (R 4.2.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.1)
processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.2)
profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.1)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.1)
ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.2)
purrr 0.3.5 2022-10-06 [1] CRAN (R 4.2.2)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.1)
radiator 1.2.4 2022-11-15 [1] Github (thierrygosselin/radiator@06ae13f)
Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
readr 2.1.3 2022-10-01 [1] CRAN (R 4.2.2)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.1)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.2.1)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.2)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.1)
seqinr 4.2-16 2022-05-19 [1] CRAN (R 4.2.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
shiny 1.7.3 2022-10-25 [1] CRAN (R 4.2.2)
stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)
stringr * 1.5.0 2022-12-02 [1] CRAN (R 4.2.2)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
tidyr 1.2.1 2022-09-08 [1] CRAN (R 4.2.1)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.2)
tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.1)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.1)
usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.1)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.1)
vctrs 0.5.0 2022-10-22 [1] CRAN (R 4.2.2)
vegan 2.6-4 2022-10-11 [1] CRAN (R 4.2.2)
vroom 1.6.0 2022-09-30 [1] CRAN (R 4.2.2)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.1)
[1] C:/Users/Admin/AppData/Local/R/win-library/4.2
[2] C:/Program Files/R/R-4.2.1/library
---------------------------------------------------------------------------------
Thank you for the help
Have a good day
Sandrine
Error while using the subsampling option in Fst_WC84()
Hi, I am interested in using the Fst_WC84() with subsampling. However, while getting familiar with your function by using datasets provided by you, I am running into the following error :
**library(assigner)
data <- data_assigner_sim_01
assigner::fst_WC84(data, filename = "Test", subsample = 36, iteration.subsample = 20)
Error: Argument 1 must have names
- stop(structure(list(message = "Argument 1 must have names", call = NULL,
cppstack = NULL), class = c("Rcpp::exception", "C++Error",
"error", "condition"))) - bind_rows_(x, .id)
- dplyr::bind_rows(res$pairwise.fst.subsample)
- eval(lhs, parent, parent)
- eval(lhs, parent, parent)
- dplyr::bind_rows(res$pairwise.fst.subsample) %>% dplyr::group_by(POP1,
POP2) %>% dplyr::summarise_all(.tbl = ., .funs = mean, na.rm = TRUE) %>%
dplyr::mutate(ITERATIONS = rep(iteration.subsample, n())) at fst_WC84.R#649 - assigner::fst_WC84(data, filename = "Test", subsample = 36, iteration.subsample = 20 )_**
I have read other reports about a similar issue, but that is all in the context of assignment analysis and not Fst calculations. Is this a bug or am I missing something here?
Thank you,
P.S. The function runs just fine without the subsampling argument.
digits in heatmap_fst()
Nothing happens when I'm trying to change argument 'digits' in heatmap_fst(), it is always 5 decimal digits on heatmap. For instance:
heatmap_fst(fst.ci$pairwise.fst.full.matrix, fst.ci$pairwise.fst.ci.matrix, n.s = TRUE,
digits = 3, color.low = "white", color.mid = "grey",
color.high = "black", text.size = 4, plot.size = 40,
pop.levels = NULL, path.folder = NULL, filename = NULL)
heatmap_fst(fst.ci$pairwise.fst.full.matrix, fst.ci$pairwise.fst.ci.matrix, n.s = TRUE,
digits = 5, color.low = "white", color.mid = "grey",
color.high = "black", text.size = 4, plot.size = 40,
pop.levels = NULL, path.folder = NULL, filename = NULL)
heatmap_fst(fst.ci$pairwise.fst.full.matrix, fst.ci$pairwise.fst.ci.matrix, n.s = TRUE,
digits = 8, color.low = "white", color.mid = "grey",
color.high = "black", text.size = 4, plot.size = 40,
pop.levels = NULL, path.folder = NULL, filename = NULL)
all three give me identical results.
There is another problem, probably related to the described above - the fst values and corresponding CI intervals are mixed between upper and lower parts of matrix on the heatmap:
Warning messages:
1: Column POP1 has different attributes on LHS and RHS of join
2: Column POP2 has different attributes on LHS and RHS of join
devtools::session_info()
─ Session info
setting value
version R version 3.6.2 (2019-12-12)
os Ubuntu 18.04.3 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Asia/Yekaterinburg
date 2020-01-07
─ Packages
package * version date lib source
ade4 * 1.7-13 2018-08-31 [1] CRAN (R 3.6.1)
adegenet * 2.1.1 2018-02-02 [1] CRAN (R 3.6.1)
ape 5.3 2019-03-17 [1] CRAN (R 3.6.1)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
assigner * 0.5.6 2019-12-08 [1] Github (b941111)
backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.1)
Biobase 2.44.0 2019-05-02 [1] Bioconductor
BiocGenerics 0.30.0 2019-05-02 [1] Bioconductor
Biostrings 2.52.0 2019-05-02 [1] Bioconductor
bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.1)
boot 1.3-24 2019-12-20 [4] CRAN (R 3.6.2)
broom 0.5.2 2019-04-07 [1] CRAN (R 3.6.1)
callr 3.3.2 2019-09-22 [1] CRAN (R 3.6.1)
class 7.3-15 2019-01-01 [4] CRAN (R 3.6.1)
classInt 0.4-2 2019-10-17 [1] CRAN (R 3.6.1)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
cluster 2.1.0 2019-06-19 [4] CRAN (R 3.6.1)
coda 0.19-3 2019-07-05 [1] CRAN (R 3.6.1)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
data.table 1.12.6 2019-10-18 [1] CRAN (R 3.6.1)
DBI 1.0.0 2018-05-02 [1] CRAN (R 3.6.1)
deldir 0.1-23 2019-07-31 [1] CRAN (R 3.6.1)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1)
devtools 2.1.0 2019-07-06 [1] CRAN (R 3.6.1)
digest 0.6.23 2019-11-23 [1] CRAN (R 3.6.1)
dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.1)
e1071 1.7-3 2019-11-26 [1] CRAN (R 3.6.1)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.1)
expm 0.999-4 2019-03-21 [1] CRAN (R 3.6.1)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.6.1)
farver 2.0.1 2019-11-13 [1] CRAN (R 3.6.1)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 3.6.1)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.1)
fst 0.9.0 2019-04-09 [1] CRAN (R 3.6.1)
gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.1)
gdsfmt 1.20.0 2019-05-02 [1] Bioconductor
generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.1)
GenomeInfoDb 1.20.0 2019-05-02 [1] Bioconductor
GenomeInfoDbData 1.2.1 2019-12-08 [1] Bioconductor
GenomicRanges 1.36.1 2019-09-06 [1] Bioconductor
ggplot2 3.2.1 2019-08-10 [1] CRAN (R 3.6.1)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
gmodels 2.18.1 2018-06-25 [1] CRAN (R 3.6.1)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.1)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.1)
gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.1)
GWASExactHW 1.01 2013-01-05 [1] CRAN (R 3.6.1)
hms 0.5.2 2019-10-30 [1] CRAN (R 3.6.1)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.1)
httpuv 1.5.2 2019-09-11 [1] CRAN (R 3.6.1)
igraph 1.2.4.2 2019-11-27 [1] CRAN (R 3.6.1)
IRanges 2.18.3 2019-09-24 [1] Bioconductor
jomo 2.6-10 2019-10-22 [1] CRAN (R 3.6.1)
KernSmooth 2.23-16 2019-10-15 [4] CRAN (R 3.6.1)
labeling 0.3 2014-08-23 [1] CRAN (R 3.6.1)
later 1.0.0 2019-10-04 [1] CRAN (R 3.6.1)
lattice 0.20-38 2018-11-04 [4] CRAN (R 3.6.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.1)
LearnBayes 2.15.1 2018-03-18 [1] CRAN (R 3.6.1)
lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.1)
lme4 1.1-21 2019-03-05 [1] CRAN (R 3.6.1)
logistf 1.23 2018-07-19 [1] CRAN (R 3.6.1)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
MASS 7.3-51.5 2019-12-20 [4] CRAN (R 3.6.2)
Matrix 1.2-18 2019-11-27 [4] CRAN (R 3.6.1)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.1)
mgcv 1.8-31 2019-11-09 [4] CRAN (R 3.6.1)
mice 3.6.0 2019-07-10 [1] CRAN (R 3.6.1)
mime 0.7 2019-06-11 [1] CRAN (R 3.6.1)
minqa 1.2.4 2014-10-09 [1] CRAN (R 3.6.1)
mitml 0.3-7 2019-01-07 [1] CRAN (R 3.6.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.1)
nlme 3.1-143 2019-12-10 [4] CRAN (R 3.6.2)
nloptr 1.2.1 2018-10-03 [1] CRAN (R 3.6.1)
nnet 7.3-12 2016-02-02 [4] CRAN (R 3.6.1)
pan 1.6 2018-06-29 [1] CRAN (R 3.6.1)
pbmcapply 1.5.0 2019-07-10 [1] CRAN (R 3.6.1)
permute 0.9-5 2019-03-12 [1] CRAN (R 3.6.1)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.1)
pinfsc50 1.1.0 2016-12-02 [1] CRAN (R 3.6.1)
pkgbuild 1.0.5 2019-08-26 [1] CRAN (R 3.6.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.1)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.1)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.1)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.1)
promises 1.1.0 2019-10-04 [1] CRAN (R 3.6.1)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.1)
purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.1)
R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1)
radiator * 1.1.2 2019-12-08 [1] Github (thierrygosselin/radiator@480ef0f)
Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.1)
RCurl 1.95-4.12 2019-03-04 [1] CRAN (R 3.6.1)
readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.1)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.1)
rlang 0.4.2 2019-11-23 [1] CRAN (R 3.6.1)
rpart 4.1-15 2019-04-12 [4] CRAN (R 3.6.1)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.1)
rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.6.1)
S4Vectors 0.22.1 2019-09-09 [1] Bioconductor
scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.1)
SeqArray 1.24.2 2019-07-12 [1] Bioconductor
seqinr 3.6-1 2019-09-07 [1] CRAN (R 3.6.1)
SeqVarTools 1.22.0 2019-05-02 [1] Bioconductor
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
sf 0.8-0 2019-09-17 [1] CRAN (R 3.6.1)
shiny 1.4.0 2019-10-10 [1] CRAN (R 3.6.1)
sp 1.3-2 2019-11-07 [1] CRAN (R 3.6.1)
spData 0.3.2 2019-09-19 [1] CRAN (R 3.6.1)
spdep 1.1-3 2019-09-18 [1] CRAN (R 3.6.1)
stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.1)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
survival 3.1-8 2019-12-03 [4] CRAN (R 3.6.2)
testthat 2.2.1 2019-07-25 [1] CRAN (R 3.6.1)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.1)
tidyr 1.0.0 2019-09-11 [1] CRAN (R 3.6.1)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.1)
units 0.6-5 2019-10-08 [1] CRAN (R 3.6.1)
UpSetR 1.4.0 2019-05-22 [1] CRAN (R 3.6.1)
usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.1)
vcfR * 1.8.0 2018-04-17 [1] CRAN (R 3.6.1)
vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.1)
vegan 2.5-6 2019-09-01 [1] CRAN (R 3.6.1)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.1)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.1)
XVector 0.24.0 2019-05-02 [1] Bioconductor
zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.1)
zlibbioc 1.30.0 2019-05-02 [1] Bioconductor
assignment_ngs error: problem with 'mutate()'
I cannot help you if I cannot reproduce the problem.
Consequently, when reporting an issue, make sure to include:
Describe the bug
assigner::assignment_ngs does not work- suspecting it is a dplyr issue. I tried dplyr v1.0.0 and the latest v1.0.4
To Reproduce
Include the steps to reproduce the behavior:
- the exact command (function, arguments, values) used
Command I ran:
assigner::assignment_ngs(
GENLIGHT391ind_3_realpop$genlight,
assignment.analysis = "gsi_sim",
markers.sampling = "ranked",
thl = 0.5,
iteration.method = 30,
adegenet.dapc.opt = "optim.a.score",
marker.number = c(2, 4, 8, 16, 32, 64, 128, 200, 500, 1000, 2000, "all"),
subsample = "min",
iteration.subsample = 3
)
- the complete error message you're getting
Error: Problem with `mutate()` input `..1`.
x Can't subset columns that don't exist.
x Column `STRATA` doesn't exist.
ℹ Input `..1` is `(function (.cols = everything(), .fns = NULL, ..., .names = NULL) ...`.
Run `rlang::last_error()` to see where the error occurred.
Computation time, overall: 7 sec
- the output of
devtools::session_info()
Strangely I have macOS11.2.2, but in the below session info it says 10.16?
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.2 (2020-06-22)
os macOS 10.16
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_CA.UTF-8
ctype en_CA.UTF-8
tz America/Toronto
date 2021-03-02
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.2)
ade4 * 1.7-16 2020-10-28 [1] CRAN (R 4.0.2)
adegenet * 2.1.3 2020-05-10 [1] CRAN (R 4.0.2)
adegraphics 1.0-15 2018-12-18 [1] CRAN (R 4.0.2)
adephylo 1.1-11 2017-12-18 [1] CRAN (R 4.0.2)
adespatial 0.3-10 2021-02-09 [1] CRAN (R 4.0.2)
ape 5.4-1 2020-08-13 [1] CRAN (R 4.0.2)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
assigner * 0.5.8 2021-02-26 [1] Github (thierrygosselin/assigner@d39a692)
backports 1.2.1 2020-12-09 [1] CRAN (R 4.0.2)
boot 1.3-25 2020-04-26 [1] CRAN (R 4.0.2)
broom 0.7.3 2020-12-16 [1] CRAN (R 4.0.2)
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.2)
car 3.0-10 2020-09-29 [1] CRAN (R 4.0.2)
carData 3.0-4 2020-05-22 [1] CRAN (R 4.0.2)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.2)
class 7.3-17 2020-04-26 [1] CRAN (R 4.0.2)
classInt 0.4-3 2020-04-07 [1] CRAN (R 4.0.2)
cli 2.2.0 2020-11-20 [1] CRAN (R 4.0.2)
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.2)
coda 0.19-4 2020-09-30 [1] CRAN (R 4.0.2)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.0.2)
colorspace 2.0-0 2020-11-11 [1] CRAN (R 4.0.2)
cowplot 1.0.0 2019-07-11 [1] CRAN (R 4.0.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.1)
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.0.1)
data.tree 1.0.0 2020-08-03 [1] CRAN (R 4.0.2)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2)
deldir 0.2-9 2021-01-16 [1] CRAN (R 4.0.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
devtools * 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
DiagrammeR 1.0.6.1 2020-05-08 [1] CRAN (R 4.0.2)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2)
dplyr * 1.0.0 2020-05-29 [1] CRAN (R 4.0.2)
e1071 1.7-3 2019-11-26 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
expm 0.999-5 2020-07-20 [1] CRAN (R 4.0.2)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.2)
forcats 0.5.0 2020-03-01 [1] CRAN (R 4.0.2)
foreign 0.8-80 2020-05-24 [1] CRAN (R 4.0.2)
fs 1.4.2 2020-06-30 [1] CRAN (R 4.0.2)
gdata 2.18.0 2017-06-06 [1] CRAN (R 4.0.2)
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2)
ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
ggpubr 0.4.0 2020-06-27 [1] CRAN (R 4.0.2)
ggsignif 0.6.0 2019-08-08 [1] CRAN (R 4.0.2)
glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.2)
gmodels 2.18.1 2018-06-25 [1] CRAN (R 4.0.2)
grur * 0.1.4 2021-02-26 [1] Github (thierrygosselin/grur@d31c423)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
gtools 3.8.2 2020-03-31 [1] CRAN (R 4.0.2)
haven 2.3.1 2020-06-01 [1] CRAN (R 4.0.2)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.2)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.2)
httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2)
igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.2)
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.0.2)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.2)
KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.2)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2)
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.0.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.2)
LearnBayes 2.15.1 2018-03-18 [1] CRAN (R 4.0.2)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)
MASS 7.3-51.6 2020-04-26 [1] CRAN (R 4.0.2)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2)
mgcv 1.8-31 2019-11-09 [1] CRAN (R 4.0.2)
mime 0.9 2020-02-04 [1] CRAN (R 4.0.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
nlme 3.1-148 2020-05-24 [1] CRAN (R 4.0.2)
openxlsx 4.1.5 2020-05-06 [1] CRAN (R 4.0.2)
permute 0.9-5 2019-03-12 [1] CRAN (R 4.0.2)
phylobase 0.8.10 2020-03-01 [1] CRAN (R 4.0.2)
pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
pinfsc50 1.2.0 2020-06-03 [1] CRAN (R 4.0.2)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
plyr * 1.8.6 2020-03-03 [1] CRAN (R 4.0.2)
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.4.5 2020-11-30 [1] CRAN (R 4.0.2)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.0.2)
promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2)
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.2)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
radiator * 1.1.9 2021-01-21 [1] Github (thierrygosselin/radiator@5c6b865)
randomForestSRC * 2.10.1 2021-02-10 [1] CRAN (R 4.0.2)
raster 3.3-13 2020-07-17 [1] CRAN (R 4.0.2)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.2)
Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
readr 1.4.0 2020-10-05 [1] CRAN (R 4.0.2)
readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.2)
remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.2)
rio 0.5.16 2018-11-26 [1] CRAN (R 4.0.2)
rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.2)
rncl 0.8.4 2020-02-10 [1] CRAN (R 4.0.2)
RNeXML 2.4.5 2020-06-18 [1] CRAN (R 4.0.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
rstatix 0.6.0 2020-06-18 [1] CRAN (R 4.0.2)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
seqinr 3.6-1 2019-09-07 [1] CRAN (R 4.0.2)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
sf 0.9-7 2021-01-06 [1] CRAN (R 4.0.2)
shiny 1.6.0 2021-01-25 [1] CRAN (R 4.0.2)
sp 1.4-5 2021-01-10 [1] CRAN (R 4.0.2)
spData 0.3.8 2020-07-03 [1] CRAN (R 4.0.2)
spdep 1.1-5 2020-06-29 [1] CRAN (R 4.0.2)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2)
tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)
tidyr 1.1.2 2020-08-27 [1] CRAN (R 4.0.2)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2)
units 0.6-7 2020-06-13 [1] CRAN (R 4.0.2)
usethis * 2.0.0 2020-12-10 [1] CRAN (R 4.0.2)
uuid 0.1-4 2020-02-26 [1] CRAN (R 4.0.2)
vcfR * 1.12.0 2020-07-28 [1] Github (knausb/vcfR@8a61e1c)
vctrs 0.3.6 2020-12-17 [1] CRAN (R 4.0.2)
vegan 2.5-6 2019-09-01 [1] CRAN (R 4.0.2)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.1)
visNetwork 2.0.9 2019-12-06 [1] CRAN (R 4.0.2)
withr 2.4.0 2021-01-16 [1] CRAN (R 4.0.2)
XML 3.99-0.5 2020-07-23 [1] CRAN (R 4.0.2)
xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.2)
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2)
zip 2.1.1 2020-08-27 [1] CRAN (R 4.0.2)
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
- complete data required to reproduce the problem, a subset of it. The data remains confidential.
radiator_genlight391ind_3_realpop.RData.zip
Screenshots
If applicable, add screenshots to help explain your problem.
problem with assignment_ngs function
Hello,
I am trying to use the assignment_ngs function on a genind object and receiving an error message.
Read in genepop file and save as genind object
my_data <-read.genepop("Herring_PopulationStructure_3001loci_301samples.gen", ncode = 2)
my_assignment <- assignment_ngs(my_data,
assignment.analysis = "gsi_sim",
sampling.method == "ranked",
thl = 1,
iteration.method = 10,
subsample = NULL,
iteration.subsample = 10,
common.markers = FALSE,
marker.number = "100",
verbose = TRUE,
folder = NULL,
filename = "assignment_data.txt",
keep.gsi.files = FALSE,
random.seed = NULL,
parallel.core = parallel::detectCores() - 1)
I am receiving the following error message:
Assignment analysis with gsi_sim
Map-independent imputations: no
Error in stringi::stri_join(getwd(), "/", "assignment_analysis_", "method_", :
object 'sampling.method' not found
I would appreciate any help that you could provide.
Best regards,
Eleni
Error: Argument 1 must have names
Hello! I am running the following code in R v3.5.1 using new installs of the radiator and assigner R packages (installed via devtools Sep 14, 2019) on my Mac:
test.tidy = radiator::tidy_genomic_data(data="test.gen", strata="subset_strata.txt")
assign1 <- assigner::assignment_ngs(
data = test.tidy,
assignment.analysis = "gsi_sim",
markers.sampling = "ranked",
thl = 0.2,
iteration.method = 5
)
I get the following error:
##################### assigner::assignment_ngs ################
Execution date/time: 20190914@1348
Assignment analysis with gsi_sim
Folder created: assignment_analysis_method_ranked_20190914@1348
Subsampling: not selected
Conducting Assignment analysis using Training, Holdout, Leave-one-out
Using training samples to rank markers based on Fst
Holdout samples saved in your folder
Starting parallel computations, for progress monitor activity in folder...
Error: Argument 1 must have names
Computation time, overall: 1 sec
###############assignment_ngs completed ############
I've attached my input files (subsets of my full dataset) so that you can recreate the issue. I am using 'test.gen' as input with the attached file, not 'test.txt' (will not let me upload with *.gen file extension). I see an earlier bug report from a user that was getting the same error but changing the file extension did not fix the problem. I've also attached the output from devtools::session_info(). I should also note that I get the same error when attempting to run the same code but using the test datasets provided in the assigner vignettes (data_assigner_sim_01, data_assigner_sim_02). Please let me know if any other information would be helpful! Thanks!
STRATA_SEQ error with assignment_ngs()
Hello,
Describe the bug
I am having issues when running assignment_ngs() on a genlight object. I load my genlight file output from dartR and get the following error message (see below). I cannot find any reference to STRATA_SEQ in the package code, so I'm having trouble figuring out what my issue is. I get the same issue when using the simulated data from the package: data_assigner_sim_01
To Reproduce
Assign <- assignment_ngs(data=data_assigner_sim_01,
assignment.analysis = "gsi_sim",
marker.number = c(50,100,200,500,1000, "all"),
markers.sampling = "ranked",
thl = 0.2,
iteration.method = 5,
subsample = 15,
iteration.subsample= 3)
Error message:
################################################################################
########################## assigner::assignment_ngs ############################
################################################################################
Execution date/time: 20230614@1021
Assignment analysis with gsi_sim
Calibrating REF/ALT alleles...
Calibrating REF/ALT alleles...
Subsampling: selected
using subsample size of: 15
Error in purrr::map():
In index: 1.
Caused by error in dplyr::group_by():
! Must group by variables found in .data.
✖ Column STRATA_SEQ is not found.
Backtrace:
- assigner::assignment_ngs(...)
- dplyr:::group_by.data.frame(., STRATA_SEQ)
Computation time, overall: 2 sec
########################## assignment_ngs completed ############################
devtools::session_info()
─ Session info
setting value
version R version 4.3.0 (2023-04-21)
os macOS Monterey 12.5.1
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2023-06-14
rstudio 2023.03.1+446 Cherry Blossom (desktop)
pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
─ Packages
package * version date (UTC) lib source
ade4 * 1.7-22 2023-02-06 [1] CRAN (R 4.3.0)
adegenet * 2.1.10 2023-01-26 [1] CRAN (R 4.3.0)
ape 5.7-1 2023-03-13 [1] CRAN (R 4.3.0)
assigner * 0.5.8 2023-06-13 [1] Github (d39a692)
bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
calibrate 1.7.7 2020-06-19 [1] CRAN (R 4.3.0)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
cluster 2.1.4 2022-08-22 [1] CRAN (R 4.3.0)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.0)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
combinat 0.0-8 2012-10-29 [1] CRAN (R 4.3.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
dartR * 2.9.7 2023-06-07 [1] CRAN (R 4.3.0)
dartR.data * 1.0.2 2022-11-16 [1] CRAN (R 4.3.0)
data.table * 1.14.8 2023-02-17 [1] CRAN (R 4.3.0)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0)
dismo 1.3-14 2023-05-21 [1] CRAN (R 4.3.0)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.3.0)
dotCall64 1.0-2 2022-10-03 [1] CRAN (R 4.3.0)
dplyr * 1.1.2 2023-04-20 [1] CRAN (R 4.3.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
evaluate 0.21 2023-05-05 [1] CRAN (R 4.3.0)
fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
fields 14.1 2022-08-12 [1] CRAN (R 4.3.0)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.3.0)
fs 1.6.2 2023-04-25 [1] CRAN (R 4.3.0)
gap 1.5-1 2023-01-22 [1] CRAN (R 4.3.0)
gap.datasets 0.0.5 2022-05-09 [1] CRAN (R 4.3.0)
gdata 2.19.0 2023-05-05 [1] CRAN (R 4.3.0)
gdistance 1.6.2 2023-04-20 [1] CRAN (R 4.3.0)
gdsfmt 1.36.0 2023-05-08 [1] Bioconductor
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
genetics 1.3.8.1.3 2021-03-01 [1] CRAN (R 4.3.0)
GGally 2.1.2 2021-06-21 [1] CRAN (R 4.3.0)
ggplot2 * 3.4.2 2023-04-03 [1] CRAN (R 4.3.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.3.0)
gtable 0.3.3 2023-03-21 [1] CRAN (R 4.3.0)
gtools 3.9.4 2022-11-27 [1] CRAN (R 4.3.0)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.0)
htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
igraph 1.4.3 2023-05-22 [1] CRAN (R 4.3.0)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.0)
knitr 1.43 2023-05-25 [1] CRAN (R 4.3.0)
later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
lattice 0.21-8 2023-04-05 [1] CRAN (R 4.3.0)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
maps 3.4.1 2022-10-30 [1] CRAN (R 4.3.0)
MASS 7.3-60 2023-05-04 [1] CRAN (R 4.3.0)
Matrix 1.5-4.1 2023-05-18 [1] CRAN (R 4.3.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
mgcv 1.8-42 2023-03-02 [1] CRAN (R 4.3.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
mmod 1.3.3 2017-04-06 [1] CRAN (R 4.3.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
mvtnorm 1.2-2 2023-06-08 [1] CRAN (R 4.3.0)
nlme 3.1-162 2023-01-31 [1] CRAN (R 4.3.0)
patchwork 1.1.2 2022-08-19 [1] CRAN (R 4.3.0)
pegas 1.2 2023-02-23 [1] CRAN (R 4.3.0)
permute 0.9-7 2022-01-27 [1] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.3.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
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ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0)
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R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
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raster 3.6-20 2023-03-06 [1] CRAN (R 4.3.0)
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shiny 1.7.4 2022-12-15 [1] CRAN (R 4.3.0)
SNPRelate 1.34.1 2023-05-08 [1] Bioconductor
sp 1.6-1 2023-05-31 [1] CRAN (R 4.3.0)
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[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
5 nodes produced errors; first error: error writing to connection
Hi Thierry,
I'm gettting the error message below when attempting to run assignment_ngs in RStudio. I read through the older issues and found one similar, but there was no resolution posted. Based on that issue though, I ran detect Cores() , which shows 8 cores, and then tried running the code with parallel.core = 1. When I run assignment_ngs with more cores, I get more nodes producing more errors (5 vs. 1). Any help would be greatly appreciated. I attached the populations folder, but it would not let me attach the vcf. Thanks in advance!
Best,
Justine Whitaker
STL.vcf2=read_vcf('STLpopulations.snps.vcf', strata = 'StLaw_popmapFINAL.txt', parallel.core = 1)
test2 <- assigner::assignment_ngs(data = STL.vcf2, assignment.analysis = "gsi_sim", markers.sampling = "ranked", thl = 0.2, iteration.method = 5, marker.number = c(100, 200, 300, 400, "all"), subsample = 20, iteration.subsample = 3, parallel.core = 1)
assigner::assignment_ngs ############################ ################################################################################ Execution date/time: 20200406@1332 Assignment analysis with gsi_sim Folder created: assignment_analysis_method_ranked_20200406@1332 Computation time, overall: 8 sec Calibrating REF/ALT alleles... number of REF/ALT switch = 21 Subsampling: selected using subsample size of: 20 Analyzing subsample: 1 Conducting Assignment analysis using Training, Holdout, Leave-one-out Using training samples to rank markers based on Fst Holdout samples saved in your folder Starting parallel computations, for progress monitor activity in folder... Error in checkForRemoteErrors(val) : one node produced an error: 'assignment_data_iteration_1_markers_100.output.txt' does not exist in current working directory ('C:/Users/justi/Documents/Fisheries Research Revisions/assignPOP/assignment_analysis_method_ranked_20200406@1332/subsample_1/assignment_1'). In addition: Warning messages: 1: In serialize(data, node$con) : 'package:stats' may not be available when loading 2: In serialize(data, node$con) : 'package:stats' may not be available when loading 3: In serialize(data, node$con) : 'package:stats' may not be available when loading 4: In serialize(data, node$con) : 'package:stats' may not be available when loading 5: In serialize(data, node$con) : 'package:stats' may not be available when loading 6: In serialize(data, node$con) : 'package:stats' may not be available when loading Computation time, overall: 118 sec ########################## assignment_ngs completed ############################
| >
parallel::detectCores()
[1] 8
devtools::session_info()
Registered S3 method overwritten by 'cli':
method from
print.tree tree
-
Session info ------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.6.3 (2020-02-29)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/Chicago
date 2020-04-06 -
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ape 5.3 2019-03-17 [1] CRAN (R 3.6.3)
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[1] C:/Users/justi/Documents/R/win-library/3.6
[2] C:/Program Files/R/R-3.6.3/library
[StLaw_popmapFINAL.txt]
(https://github.com/thierrygosselin/assigner/files/4440233/StLaw_popmapFINAL.txt)
Error in checkForRemoteErrors(val) : 3 nodes produced errors
Describe the bug
When I tried to work through the first example on http://thierrygosselin.github.io/assigner/articles/get_started.html (Data 1: high structure), I always got the following error messages (see below).
To Reproduce
Include the steps to reproduce the behavior:
- the exact command (function, arguments, values) used:
test1 <- assigner::assignment_ngs(
data = data,
assignment.analysis = "gsi_sim",
markers.sampling = "ranked",
thl = 0.2,
iteration.method = 5
)
- the complete error message you're getting
Error in checkForRemoteErrors(val) :
3 nodes produced errors; first error: 'assignment_data_iteration_1_markers_497.output.txt' does not exist in current working directory ('C:/Users/gp/Documents/assignment_analysis_method_ranked_20190808@1453/assignment_1').
In addition: There were 18 warnings (use warnings() to see them)
Computation time, overall: 577 sec
########################## assignment_ngs completed ############################
warnings()
Warnmeldungen:
1: In serialize(data, node$con) :
'package:stats' may not be available when loading
2: In serialize(data, node$con) :
'package:stats' may not be available when loading
3: In serialize(data, node$con) :
'package:stats' may not be available when loading
4: In serialize(data, node$con) :
'package:stats' may not be available when loading
5: In serialize(data, node$con) :
'package:stats' may not be available when loading
6: In serialize(data, node$con) :
'package:stats' may not be available when loading
7: In serialize(data, node$con) :
'package:stats' may not be available when loading
8: In serialize(data, node$con) :
'package:stats' may not be available when loading
9: In serialize(data, node$con) :
'package:stats' may not be available when loading
10: In serialize(data, node$con) :
'package:stats' may not be available when loading
11: In serialize(data, node$con) :
'package:stats' may not be available when loading
12: In serialize(data, node$con) :
'package:stats' may not be available when loading
13: In serialize(data, node$con) :
'package:stats' may not be available when loading
14: In serialize(data, node$con) :
'package:stats' may not be available when loading
15: In serialize(data, node$con) :
'package:stats' may not be available when loading
16: In serialize(data, node$con) :
'package:stats' may not be available when loading
17: In serialize(data, node$con) :
'package:stats' may not be available when loading
18: In serialize(data, node$con) :
'package:stats' may not be available when loading
(truncated here)
- the output of
devtools::session_info()
devtools::session_info()
-
Session info --------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.6.1 (2019-07-05)
os Windows 7 x64 SP 1
system x86_64, mingw32
ui RStudio
language (EN)
collate German_Switzerland.1252
ctype German_Switzerland.1252
tz Europe/Berlin
date 2019-08-08 -
Packages ------------------------------------------------------------------------------------------------------------------------------------
package * version date lib source
ade4 1.7-13 2018-08-31 [1] CRAN (R 3.6.1)
adegenet 2.1.1 2018-02-02 [1] CRAN (R 3.6.1)
ape 5.3 2019-03-17 [1] CRAN (R 3.6.1)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
assigner * 0.5.6 2019-08-08 [1] Github (b941111)
backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
boot 1.3-22 2019-04-02 [2] CRAN (R 3.6.1)
callr 3.3.1 2019-07-18 [1] CRAN (R 3.6.1)
class 7.3-15 2019-01-01 [2] CRAN (R 3.6.1)
classInt 0.3-3 2019-04-26 [1] CRAN (R 3.6.1)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
cluster 2.1.0 2019-06-19 [2] CRAN (R 3.6.1)
coda 0.19-3 2019-07-05 [1] CRAN (R 3.6.1)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
curl 4.0 2019-07-22 [1] CRAN (R 3.6.1)
DBI 1.0.0 2018-05-02 [1] CRAN (R 3.6.1)
deldir 0.1-23 2019-07-31 [1] CRAN (R 3.6.1)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1)
devtools * 2.1.0 2019-07-06 [1] CRAN (R 3.6.1)
digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.1)
dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.1)
e1071 1.7-2 2019-06-05 [1] CRAN (R 3.6.1)
expm 0.999-4 2019-03-21 [1] CRAN (R 3.6.1)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.1)
gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.0)
ggplot2 3.2.0 2019-06-16 [1] CRAN (R 3.6.0)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
gmodels 2.18.1 2018-06-25 [1] CRAN (R 3.6.1)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.1)
gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0)
hms 0.5.0 2019-07-09 [1] CRAN (R 3.6.1)
htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.1)
httpuv 1.5.1 2019-04-05 [1] CRAN (R 3.6.1)
igraph 1.2.4.1 2019-04-22 [1] CRAN (R 3.6.1)
KernSmooth 2.23-15 2015-06-29 [2] CRAN (R 3.6.1)
later 0.8.0 2019-02-11 [1] CRAN (R 3.6.1)
lattice 0.20-38 2018-11-04 [2] CRAN (R 3.6.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.1)
LearnBayes 2.15.1 2018-03-18 [1] CRAN (R 3.6.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
MASS 7.3-51.4 2019-03-31 [2] CRAN (R 3.6.1)
Matrix 1.2-17 2019-03-22 [2] CRAN (R 3.6.1)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.1)
mgcv 1.8-28 2019-03-21 [2] CRAN (R 3.6.1)
mime 0.7 2019-06-11 [1] CRAN (R 3.6.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.1)
nlme 3.1-140 2019-05-12 [2] CRAN (R 3.6.1)
pbmcapply 1.5.0 2019-07-10 [1] CRAN (R 3.6.1)
permute 0.9-5 2019-03-12 [1] CRAN (R 3.6.1)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.1)
pkgbuild 1.0.4 2019-08-05 [1] CRAN (R 3.6.1)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.6.1)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.1)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.1)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.1)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.1)
promises 1.0.1 2018-04-13 [1] CRAN (R 3.6.1)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.1)
purrr 0.3.2 2019-03-15 [1] CRAN (R 3.6.1)
R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.1)
radiator 1.1.1 2019-08-08 [1] Github (thierrygosselin/radiator@d79b062)
Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.1)
readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.1)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.1)
rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.1)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.1)
rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.6.1)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.6.1)
seqinr 3.4-5 2017-08-01 [1] CRAN (R 3.6.1)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
sf 0.7-7 2019-07-24 [1] CRAN (R 3.6.1)
shiny 1.3.2 2019-04-22 [1] CRAN (R 3.6.1)
sp 1.3-1 2018-06-05 [1] CRAN (R 3.6.1)
spData 0.3.0 2019-01-07 [1] CRAN (R 3.6.1)
spdep 1.1-2 2019-04-05 [1] CRAN (R 3.6.1)
stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
testthat 2.2.1 2019-07-25 [1] CRAN (R 3.6.1)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.1)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.1)
units 0.6-3 2019-05-03 [1] CRAN (R 3.6.1)
usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.1)
vegan 2.5-5 2019-05-12 [1] CRAN (R 3.6.1)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.1)
zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.1)
[1] C:/Users/gp/Documents/R/win-library/3.6
[2] C:/Program Files/R/R-3.6.1/library
- complete data required to reproduce the problem, a subset of it. The data remains confidential.
data set from the example, obtained via the command
data <- data_assigner_sim_01
Screenshots
Release assigner 1.0.0
Prepare for release:
- Check that description is informative
- Check licensing of included files
-
usethis::use_cran_comments() -
radiatoraccepted on CRAN - remove Remotes in
DESCRIPTION -
devtools::check() -
devtools::check_win_devel() -
rhub::check_for_cran() - Polish pkgdown reference index
- Draft blog post
Submit to CRAN:
-
usethis::use_version('major') - Update
cran-comments.md -
devtools::submit_cran() - Approve email
Wait for CRAN...
- Accepted 🎉
-
usethis::use_github_release() -
usethis::use_dev_version() -
usethis::use_news() - Update install instructions in README
- Finish blog post
- Tweet
- Add link to blog post in pkgdown news menu
Error: object "MARKERS" not found
I am trying to re-run some analyses that I did a few months ago, using assigner with gsi_sim in RStudio on a linux machine. After installing assigner and gsi_sim from within RStudio and then attempting to run the function assignment_ngs, I am receiving the error message:
Error in mutate_impl(.data, dots) : Evaluation error: object 'MARKERS' not found.
I have tried removing and re-installing assigner and gsi_sim, as well as each required package. I have checked my genepop file to make sure that the error is not in my input file, and all seems fine. I'm at a bit of a loss as to what the error message means; any help is much appreciated! I attached the code that I am working with for reference.
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