FarmCPU not running

[sjclare]

Hi,

I'm running GWAS on new phenotypes but I use a control phenotype to check the results are reliable. We were able to get some new marker positions and imputed more missing data so I expected the results to improve however now I get errors, though only on FarmCPU. GLM and BLINK both work the way we expect, except to be the top the markers is the second best but that is like the previous run, I've also gone back to the original data, before the updated marker positions and imputation and get the same error.

This is similar to #98, but I have got any help there

[1] "--------------------- Welcome to GAPIT ----------------------------"
[1] "FarmCPU"
[1] "--------------------Processing traits----------------------------------"
[1] "Phenotype provided!"
[1] "The 1 model in all."
[1] "FarmCPU"
[1] "GAPIT.DP in process..."
[1] "Converting genotype..."
[1] "Converting HapMap format to numerical under model of Middle"
[1] "Perform numericalization"
[1] "Succesfuly finished converting HapMap which has bits of 2"
[1] "Converting genotype done."
[1] "GAPIT will filter marker with MAF setting !!"
[1] "The markers will be filtered by SNP.MAF: 0"
maf_index
TRUE
522
[1] "Filting marker for GAPIT.Genotype.View function ..."
[1] "The average distance between markers are ..."
[1] NA NA NA NA NA NA
[1] "GAPIT.Genotype.View . pdfs generate.successfully!"
NULL
[1] "GAPIT.DP accomplished successfully for multiple traits. Results are saved"
[1] "Processing trait: Row"
[1] "GAPIT.Phenotype.View in press..."
[1] "GAPIT.Phenotype.View output pdf has been generated successfully!"
[1] "--------------------Phenotype and Genotype ----------------------------------"
[1] "FarmCPU"
[1] TRUE
[1] "There are 1 traits in phenotype data."
[1] "There are 282 individuals in phenotype data."
[1] "There are 522 markers in genotype data."
[1] "Phenotype and Genotype are test OK !!"
[1] "--------------------GAPIT Logical Done----------------------------------"
[1] "GAPIT.IC in process..."
[1] "There is 0 Covarinces."
[1] "There are 282 common individuals in genotype , phenotype and CV files."
[1] "The dimension of total CV is "
[1] 282 2
[1] "GAPIT.IC accomplished successfully for multiple traits. Results are saved"
[1] "GAPIT.SS in process..."
[1] "GAPIT will be into GWAS approach..."
[1] "FarmCPU"
[1] "The GAPIT would go into Bus..."
[1] "--------------------- Welcome to FarmCPU ----------------------------"
[1] "FarmCPU Started..."
[1] "Current loop: 1 out of maximum of 10"
[1] "seqQTN"
NULL
[1] "scanning..."
[1] "number of covariates in current loop is:"
[1] 0
[1] "Current loop: 2 out of maximum of 10"
[1] "optimizing possible QTNs..."
[1] "seqQTN"
[1] 21 443 109 341 468 38 235 268 54 425
[1] "scanning..."
[1] "number of covariates in current loop is:"
[1] 10
[1] "Current loop: 3 out of maximum of 10"
[1] "optimizing possible QTNs..."
Error in if (seqQTN.save != 0 & seqQTN.save != -1 & !is.null(seqQTN)) seqQTN = union(seqQTN, :
the condition has length > 1
In addition: There were 50 or more warnings (use warnings() to see the first 50)

[jiabowang]

There are too less markers in all genotype date to the FarmCPU can not select seqQTN.

[sjclare]

So is there now a minimum number of markers for FarmCPU? What is the minimum since not even my previous data that worked doesn't work anymore

[jiabowang]

Could you share your data with me ?

[sjclare]

GM, Combo_GD2 and Row_PD are the new data files. Hapmap_final and Row are the old data files

Combo_GD2.txt
GM.txt
Row_PD.txt
Hapmap_final.txt
Row.txt

[jiabowang]

Thanks for your data. After testing, I have not any error. Here is my code and the function I used.
setwd("/Users/Jiabo/Documents/gapit/test/sjclare")
source("/Users/Jiabo/Documents/gapit/gapit_functions.txt")

myY=read.table(file="Row.txt", head = TRUE)
myG=read.table(file="Hapmap_final.txt", head = FALSE)

myGAPIT=GAPIT(
G=myG,
file.output=T
)

write.table(myGAPIT$GD,"sjclare.GD.txt",row.names=F,quote=F)
write.table(myGAPIT$GM,"sjclare.GM.txt",row.names=F,quote=F)

myGD=myGAPIT$GD
myGM=myGAPIT$GM

myGAPIT=GAPIT(
Y=myY,
GD=myGD,#[,c(TRUE,index)],
GM=myGM,#[index,],
PCA.total=3,
model=c("FarmCPU"),
file.output=T
)
gapit_functions.txt

[sjclare]

Okay, it works with your gapit_functions.txt file but not when I source from "http://zzlab.net/GAPIT/gapit_functions.txt"

[jiabowang]

seems like the file in ZZlab was not updated.
I will make it works.
Thanks.