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whitlock / OutFLANK

A procedure to find Fst outliers based on an inferred distribution of neutral Fst
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NumberOfSamples error help #26

Open EveTC opened 4 years ago

EveTC commented 4 years ago

Hi,

I am receiving the same error as @katymoo on this chain. I commente on this chain but it hasn't been active since 2017, so I thought it may be best to create a new one. Did anyone find a solution to this error?

I have made sure to include the number of populations in the NumberOfSamples argument as so:

sw_out <- OutFLANK(FstDataFrame=sw.Fs, LeftTrimFraction=0.05, RightTrimFraction=0.05, Hmin=0.1, NumberOfSamples=36, qthreshold=0.1)

but it outputs this error:

Error in optim(NumberOfSamples, localNLLAllData, lower = 2, method = "L-BFGS-B") :
  L-BFGS-B needs finite values of 'fn'

I also recieve the same error message when I set the argument to the number of individuals. Is there a limit to how many popualtion OutFLANK can handle?

Any help would be greatly appreciated! Thanks, Eve

jcaccavo commented 1 year ago

I am experiencing the same error as Eve, and as recounted in #8 .

I created my input file as follows: My .vcf file was converted to a .raw file using PLINK, with the following code: plink -vcf 3_subarea_p3_p1r0.6singleSNP_populations.snps.SORTED_min10max120miss0.75_1SNPperlocus.vcf --double-id --allow-extra-chr --set-missing-var-ids @:# --make-bed --recodeAD --out 3_subarea_p3_p1r0.6singleSNP_populations.snps.SORTED_min10max120miss0.75_1SNPperlocus.raw

I then transformed the .raw file into a genlight object in R using the function read.PLINK dm_all_ade <- read.PLINK("3_subarea_p3_p1r0.6singleSNP_populations.snps.SORTED_min10max120miss0.75_1SNPperlocus.raw")

I then transformed the genlight object into an FstDataFrame using the following code:

gl <- dm_all_ade
SNPmat <- as.matrix(gl)
colnames(SNPmat) <- NULL
row.names(SNPmat) <- NULL
SNPmat[is.na(SNPmat)] <- 9
FstDataFrame <- OutFLANK::MakeDiploidFSTMat(SNPmat, gl@loc.names,
                                            as.character(gl@pop))

Then, when trying to run OutFLANK, I ran into the same error as Eve, and as described in #8 .

Outliers <- OutFLANK::OutFLANK(FstDataFrame, NumberOfSamples = length(levels(gl@pop)),
                               qthreshold = 0.01, LeftTrimFraction = 0.01,
                               RightTrimFraction = 0.1,
                               Hmin = 0.0001)
Error in optim(NumberOfSamples, localNLLAllData, lower = 2, method = "L-BFGS-B") : 
  L-BFGS-B needs finite values of 'fn'

Any assistance on this issue would be greatly appreciated!

My R session info is as follows: devtools::session_info()

─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.2 (2022-10-31)
 os       macOS Monterey 12.6
 system   x86_64, darwin17.0
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Paris
 date     2023-02-07
 rstudio  2022.12.0+353 Elsbeth Geranium (desktop)
 pandoc   2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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 [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library

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