timothyfrasier
commented
7 months ago Hi Cristian:
I'm sorry that you are having this problem. Can you send my one of your input files (that is giving you this error) and I can see if anything jumps out?
-Tim
Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca
From: cristianP04 @.> Sent: Thursday, November 30, 2023 1:27 PM To: timothyfrasier/related @.> Cc: Subscribed @.***> Subject: [timothyfrasier/related] Program stoped in subroutine StopOnDataError (Issue #19)
Hi Timoty,
I have a dataset of 730 individuals from 13 populations which were genotyped for 13 loci (I do have some missing data). populations have different sample sizes (from 7 individuals up to 260).
I subdivided my complete dataset into 13 sub-datasets corresponding to the 13 populations to calculate the TrioML coefficient of inbreeding for each population using the coancestry function, please see below:
list and read files paths
listoffile <- list.files(path = ".", pattern = ".txt", full.names = T) pops <- lapply(listoffile, readgenotypedata) pops <- pops[c(7,10)]
Initiate an empty variable the same lenght as pops vector
inbreed_coeff <- vector("list", length(pops))
for (i in 1:length(pops)) {
Calculate the TrioML coefficient of inbreeding for each individuals
coancestry_results <- coancestry(genotype.data = pops[[i]]$gdata, trioml = 2, ci95.num.bootstrap = 100L, allow.inbreeding = F, output.file = FALSE)
Report inbreeding results for each population instead of the NULL
inbreed_coeff[[i]] <- coancestry_results$inbreeding }
However, I am getting the following error:
The observed # alleles at each locus should be in range [1,127]! Errors in DATA. Insufficient data or incorrect format. Please check DATA and format and then re-run the program Program stoped in subroutine StopOnDataError Error in system.time(.Fortran("related", PACKAGE = "related")) : Related encountered a fatal error. Timing stopped at: 0.78 1.222 2.034
I tried to run the function coancestry for all the populations separately and the error is given just for two populations that happen to have missing data for all the samples in one locus (the last one).
How can I fix this?
Thank you in advance for your help
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cristianP04
Hi Timoty,
I have a dataset of 730 individuals from 13 populations which were genotyped for 13 loci (I do have some missing data). populations have different sample sizes (from 7 individuals up to 260).
I subdivided my complete dataset into 13 sub-datasets corresponding to the 13 populations to calculate the TrioML coefficient of inbreeding for each population using the coancestry function, please see below:
listoffile <- list.files(path = ".", pattern = ".txt", full.names = T) pops <- lapply(listoffile, readgenotypedata)
inbreed_coeff <- vector("list", length(pops))
for (i in 1:length(pops)) { coancestry_results <- coancestry(genotype.data = pops[[i]]$gdata, trioml = 2, ci95.num.bootstrap = 100L, allow.inbreeding = F, output.file = FALSE) inbreed_coeff[[i]] <- coancestry_results$inbreeding }
However, I am getting the following error:
The observed # alleles at each locus should be in range [1,127]! Errors in DATA. Insufficient data or incorrect format. Please check DATA and format and then re-run the program Program stoped in subroutine StopOnDataError Error in system.time(.Fortran("related", PACKAGE = "related")) : Related encountered a fatal error. Timing stopped at: 0.78 1.222 2.034
I tried to run the function coancestry for all the populations separately and the error is given just for two populations that happen to have missing data for all the samples in one locus (the last one).
How can I fix this?
Thank you in advance for your help