error message: error in if (seqQTN.save != 0 & seqQTN.save != -1 & !is.null(seqQTN)) seqQTN = union(seqQTN, condition has length >1

[martinh19]

Dear Mr. Zhou,

I was running a GWAS on fitness - related traits of Spirodela polyrhiza using the Blink method via GAPIT. Blink is starting properly but after the 3rd iteration I am receiving the following error message (see below). Do you know the meaning of this error message and how to debug it? Thank you very much for your help!

[1] "----------------------Welcome to Blink----------------------"
[1] "----------------------Iteration: 1 ----------------------"
[1] "seqQTN:"
NULL
[1] "----------------------Iteration: 2 ----------------------"
[1] "LD remove is working...."
[1] "Number SNPs for LD remove:"
[1] 9
[1] "Model selection based on BIC is working...."
[1] "Number of SNPs for BIC selection:"
[1] 7
[1] "seqQTN:"
[1] 166092 220862 153378 510796 298770
[1] "----------------------Iteration: 3 ----------------------"
[1] "LD remove is working...."
[1] "Number SNPs for LD remove:"
[1] 8
[1] "Model selection based on BIC is working...."
[1] "Number of SNPs for BIC selection:"
[1] 8
error in if (seqQTN.save != 0 & seqQTN.save != -1 & !is.null(seqQTN)) seqQTN = union(seqQTN, :
condition has length > 1

[YaoZhou89]

I am sorry I can't trace the potential bug from the information provided here. I have no experience with such an error before. It would be better if you could provide demo data and the code you run that can repeat this error.

[martinh19]

Thank you for your answer. You find the demo data set in the attachment. Your help is very much appreciated.

best wishes

Martin
GWAS_Example_data.zip

[martinh19]

You could simply run the R script, that you will find in the example data set it is called GWAS.R. I was using GAPIT version 3.2 that you will find as in the example dataset as well. best wishes Martin

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________________________________ Von: Yao Zhou ***@***.***> Gesendet: Freitag, 14. Oktober 2022 15:52:45 An: YaoZhou89/BLINK Cc: Höfer, Martin; Author Betreff: Re: [YaoZhou89/BLINK] error message: error in if (seqQTN.save != 0 & seqQTN.save != -1 & !is.null(seqQTN)) seqQTN = union(seqQTN, condition has length >1 (Issue #9) Thanks! How can I repeat the bug? — Reply to this email directly, view it on GitHub<#9 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A3R2LJACPLQVRYPB27QSJNDWDFQS3ANCNFSM6AAAAAARCRPOR4>. You are receiving this because you authored the thread.Message ID: ***@***.***>