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jiabowang / GAPIT

Genome Association Predict Integrate Tools
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Error: object 'mysimulation' not found and Error: object 'FALS' not found #129

Open sujee119 opened 5 months ago

sujee119 commented 5 months ago

Hi,

I used GAPIT few months ago and it worked perfectly, Now i ran GAPIT functions after getting new data and these errors pops out. I tried using the old data as it is, but same happens. Please Help!

library("GAPIT") geno <- read.csv("geno_rice.csv", head = FALSE) #local folder (source=http://zzlab.net/GAPIT/data/mdp_traits.txt) pheno <- read.csv("rca.csv", head = TRUE) #local folder source=http://zzlab.net/GAPIT/data/mdp_genotype_test.hmp.txt) Gapitdata <- GAPIT( Y=pheno, G=geno, PCA.total=5, SNP.MAF=0.05, Multiple_analysis= TRUE, model=c("GLM","MLM","SUPER","MLMM","FarmCPU","Blink"), Random.model=FALS ) [1] "--------------------- Welcome to GAPIT ----------------------------" [1] "GLM" "MLM" "SUPER" "MLMM" "FarmCPU" "Blink" [1] "--------------------Processing traits----------------------------------" [1] "Phenotype provided!" [1] "The 1 model in all." [1] "GLM" [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: 0.05" maf_index FALSE TRUE 12473 21803 [1] "Calculating kinship..." [1] "Number of individuals and SNPs are 288 and 21803" [1] "Calculating ZHANG relationship defined by Zhiwu Zhang..." [1] "substracting mean..." [1] "Getting X'X..." [1] "Adjusting..." [1] "Adjustment by the minimum diagonal" [1] "Calculating kinship with Zhang method: done" [1] "kinship calculated" [1] "Creating heat map for kinship..." [1] "Kinship heat map created" [1] "Adding IDs to kinship..." [1] "Writing kinship to file..." [1] "Kinship save as file" [1] "Kinship created!" [1] "Calling prcomp..." [1] "Creating PCA graphs..." [1] "Joining taxa..." [1] "Exporting PCs..." [1] "PC created" [1] "Filting marker for GAPIT.Genotype.View function ..." [1] "GAPIT.Genotype.View . pdfs generate.successfully!" [1] 288 6 [1] "GAPIT.DP accomplished successfully for multiple traits. Results are saved" Error: object 'FALS' not found In addition: There were 50 or more warnings (use warnings() to see the first 50)

myGAPIT <- GAPIT( Y=pheno, G=geno, model=c("GLM","MLM","SUPER","MLMM","FarmCPU","Blink"), PCA.total=3, NJtree.group=4, QTN.position=mysimulation$QTN.position, Inter.Plot=TRUE, Multiple_analysis=TRUE, PCA.3d=TRUE, file.output=T ) [1] "--------------------- Welcome to GAPIT ----------------------------" [1] "GLM" "MLM" "SUPER" "MLMM" "FarmCPU" "Blink" [1] "--------------------Processing traits----------------------------------" [1] "Phenotype provided!" [1] "The 1 model in all." [1] "GLM" [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 34276 [1] "Calculating kinship..." [1] "Number of individuals and SNPs are 288 and 34276" [1] "Calculating ZHANG relationship defined by Zhiwu Zhang..." [1] "substracting mean..." [1] "Getting X'X..." [1] "Adjusting..." [1] "Adjustment by the minimum diagonal" [1] "Calculating kinship with Zhang method: done" [1] "kinship calculated" [1] "Creating heat map for kinship..." [1] "Kinship heat map created" [1] "Creating NJ Tree for kinship..." [1] "Kinship NJ TREE PDF created!" [1] "Adding IDs to kinship..." [1] "Writing kinship to file..." [1] "Kinship save as file" [1] "Kinship created!" [1] "Calling prcomp..." [1] "Creating PCA graphs..." Loading required package: rgl This build of rgl does not include OpenGL functions. Use rglwidget() to display results, e.g. via options(rgl.printRglwidget = TRUE). Loading required package: rglwidget The functions in the rglwidget package have been moved to rgl. Loading required package: htmltools Loading required package: manipulateWidget [1] "Joining taxa..." [1] "Exporting PCs..." [1] "PC created" [1] "Filting marker for GAPIT.Genotype.View function ..." [1] "GAPIT.Genotype.View . pdfs generate.successfully!" [1] 288 4 [1] "GAPIT.DP accomplished successfully for multiple traits. Results are saved" Error: object 'mysimulation' not found In addition: There were 50 or more warnings (use warnings() to see the first 50)

jiabowang commented 4 months ago

Hi, From your report, I can not find "QTN.position=mysimulation$QTN.position".