Getting coverage: Error in Y[, 1:5] : subscript out of bounds

[ramonv...@gmail.com]

Hello Yuchao,

Hope this question reach you well.

I'm getting this error when the getting covarage analysis starts:

[...]

Getting mappability for chr7

Getting mappability for chr8

Getting mappability for chr9

Getting mappability for chrX

Getting mappability for chrY

Getting coverage for sample 101.sor: read length 150.

Error in Y[, 1:5] : subscript out of bounds

Calls: head

Execution halted

How can I resolve this?

Best regards,

Ramon

[Yuchao Jiang]

Can you provide the full input and output? How many samples did you have? CODEX/CODEX2 rehires at least around 20 samples

--
You received this message because you are subscribed to the Google Groups "CODEX/CODEX2 for CNV detection" group.
To unsubscribe from this group and stop receiving emails from it, send an email to codex2+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/codex2/2a159e11-83b8-48a2-ac7a-00429e349715%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[ramonv...@gmail.com]

This is my code line:

##CODEX2 TEST- 09/07

#Pre-processing

library(CODEX2)

#library(WES.1KG.WUGSC) # Load Toy data from the 1000 Genomes Project.

dirPath <- "/home/scratch60/ramon_CODEX/bams"

bamFile <- list.files(dirPath, pattern = '101.sorted.q30.dedup.bam$')

bamdir <- file.path(dirPath, bamFile)

sampname <- substr(bamFile,1,7)

bedFile <- file.path ("/home/scratch60/ramon_CODEX/reference/S06588914_Regions-hg38.main.bed")

bambedObj <- getbambed(bamdir = bamdir, bedFile = bedFile,

                       sampname = sampname, projectname = "CODEX2_bcg")

bamdir <- bambedObjbamdir;sampname<−bambedObjbamdir;sampname<−bambedObjsampname

ref <- bambedObjref;projectname<−bambedObjref;projectname<−bambedObjprojectname

The other parts of the code remais unchanged and I am using only one BAM file and it's respective BAI file.

Em segunda-feira, 8 de julho de 2019 11:22:31 UTC-3, Yuchao Jiang escreveu:

Can you provide the full input and output? How many samples did you have? CODEX/CODEX2 rehires at least around 20 samples

On Jul 8, 2019, at 10:21 AM, ramonv...@gmail.com wrote:

Hello Yuchao,

Hope this question reach you well.

I'm getting this error when the getting covarage analysis starts:

[...]

Getting mappability for chr7

Getting mappability for chr8

Getting mappability for chr9

Getting mappability for chrX

Getting mappability for chrY

Getting coverage for sample 101.sor: read length 150.

Error in Y[, 1:5] : subscript out of bounds

Calls: head

Execution halted

How can I resolve this?

Best regards,

Ramon

--
You received this message because you are subscribed to the Google Groups "CODEX/CODEX2 for CNV detection" group.

To unsubscribe from this group and stop receiving emails from it, send an email to cod...@googlegroups.com.

[Yuchao Jiang]

Like I said, Y[,1:5] is to get the first five samples/bams and you only have one, which leads to the error

To unsubscribe from this group and stop receiving emails from it, send an email to codex2+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/codex2/32264d73-8798-40c0-b517-6e833bc0bab7%40googlegroups.com.

[ramonv...@gmail.com]

Thanks for the answers Yuchao! I was able to complete the analysis!

Cheers,

Ramon