HMM Segmentation Error "memory not mapped"

[chatterjee89]

Hi, can you tell me what might have caused this segmentation fault? I do realize this may not have been a CaSpER issue, but I have no idea what caused this, or how I can find it:

> final.objects <- runCaSpER(object, removeCentromere=T, cytoband=cytoband, method="iterative")
Performing recursive median filtering...
Performing HMM segmentation...

 *** caught segfault ***
address 0x30, cause 'memory not mapped'

Traceback:
 1: aperm(output$xi, c(3, 2, 1))
 2: is.data.frame(x)
 3: colSums(aperm(output$xi, c(3, 2, 1)))
 4: t(colSums(aperm(output$xi, c(3, 2, 1))))
 5: manualSegment(correctOut$copy, chr, autosomes, param, maxiter,     verbose)
 6: HMMsegment(correctOut = rdata, param = object@hmmparam, verbose = F)
 7: PerformSegmentationWithHMM(object, cnv.scale = i, removeCentromere = T,     cytoband = cytoband)
 8: runCaSpER(object, removeCentromere = T, cytoband = cytoband,     method = "iterative")

Thanks for a useful tutorial and otherwise a pretty easy-to-use tool btw!

Regards, Deep

[akdess]

Hi @chatterjee89, I am very sorry about the late reply. Thanks a lot for your interest!

Please let me know if you have resolved the memory issue.

Best, Akdes

[singha30]

Hello @akdess I am also facing some issues like @chatterjee89 so can any of you please help me out

[anastasija-jakjimovska]

Hi @akdess, I am having the same problem.. I made sure that I have enough memory, I use the correct R version, and that the variables and data sets are all in the correct format. Does anyone know how I can resolve this? @chatterjee89 @singha30