GAPIT 3: Error in count.temp[, 2] : subscript out of bounds

[Samrath0402]

Getting the following error during the analysis, not able to complete the analysis

Error in count.temp[, 2] : subscript out of bounds In addition: Warning messages: 1: 'memory.size()' is no longer supported 2: 'memory.size()' is no longer supported 3: 'memory.size()' is no longer supported --   > | > >

[jiabowang]

Please post more details when the GAPIT stopped.

[Samrath0402]

#Step 1: Set data directory and import files> myY <- read.table("pheno2020.hmp", head = TRUE)> myG <- read.delim("rbosnp.hmp", head = FALSE)> #Step 1: Import data> myY <- read.table("pheno2020.hmp", head = TRUE)> myG <- read.table("rbosnp.hmp" , head = FALSE)> setwd()Error in setwd() : argument "dir" is missing, with no default> myG <- read.table("rbosnp.hmp", head = FALSE)> myGAPIT <- GAPIT(G=myG, output.numerical=TRUE)[1] "--------------------- Welcome to GAPIT ----------------------------" [1] "MLM" [1] "Converting genotype..." [1] "Converting HapMap format to numerical under model of Middle" [1] "Perform numericalization"Error in count.temp[, 2] : subscript out of bounds In addition: Warning messages: 1: 'memory.size()' is no longer supported 2: 'memory.size()' is no longer supported 3: 'memory.size()' is no longer supported

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On Thu, Oct 17, 2024 at 7:14 AM Jiabo Wang ***@***.***> wrote: Please post more details when the GAPIT stopped. — Reply to this email directly, view it on GitHub <#155 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BAJZHISTMOP4MTPBK2UDQF3Z34JAFAVCNFSM6AAAAABPRNZCWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJYGMYTSMJYGY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[jiabowang]

Could you use the newest GAPIT function? I think I have fixed this error yet.

[Samrath0402]

Kindly share the link for newest GAPIT function,as i was not able to find it

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On Mon, 21 Oct, 2024, 07:52 Jiabo Wang, ***@***.***> wrote: Could you use the newest GAPIT function? I think I have fixed this error yet. — Reply to this email directly, view it on GitHub <#155 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BAJZHIR7RY3Y3RVMQGIMOP3Z4RQNHAVCNFSM6AAAAABPRNZCWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRVGQZDGNBSGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[jiabowang]

https://zzlab.net/GAPIT/index.html
or https://github.com/jiabowang/GAPIT/tree/master/R

[Samrath0402]

I will try this and get back to you, thank you so much.

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On Mon, 21 Oct, 2024, 07:59 Jiabo Wang, ***@***.***> wrote: https://zzlab.net/GAPIT/index.html or https://github.com/jiabowang/GAPIT/tree/master/R — Reply to this email directly, view it on GitHub <#155 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BAJZHIUAFOQZ6I6RUT72FYTZ4RRJ3AVCNFSM6AAAAABPRNZCWCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRVGQZTANZVGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[somnya]

Hi all,
I am having a similar issue. I would appreciate your update!

[Samrath0402]

getting this on using the R script of GAPIT 3.5
Please help