Question

'Killed' error during RNAseq alignment

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Sukeerthi • 0

@fea7fd29

Last seen 9 months ago

India

I am trying to align RNA sequencing data using the following code. However, it shows an error killed at the end. It does not specify the reason as well. I initially assumed memory could have been an issue, but the error seems to continue even when the memory issue was sorted in a new system. This is my code. Any help would be greatly appreciated.

myExons <- exons(TxDb.Hsapiens.UCSC.hg19.knownGene, columns = c("tx_id", "gene_id"))
myExons <- myExons[lengths(myExons$gene_id) == 1]
myExons

dfExons <- as.data.frame(myExons)
SAF <- data.frame(GeneID = dfExons$gene_id, Chr = dfExons$seqnames, Start = dfExons$start,
    End = dfExons$end, Strand = dfExons$strand)

This is the error message I am receiving

subjunc data.frame myExons Rsubread • 574 views

ADD COMMENT • link updated 10 months ago by ATpoint ★ 4.0k • written 10 months ago by Sukeerthi • 0

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As you can see in the output, some columns in this GRanges object are character vectors, others are lists, so this cannot readily be parsed into a meaningful data.frame, that is why it takes long and crashes. Your code does not do any alignment, so why don't you state what the end goal is so one can suggest better code to avoid these issues. Do you want to make a tx2gene map for tximport?

ADD REPLY • link 10 months ago ATpoint ★ 4.0k

score 0 · Answer 1 · 2023-06-21

Neither your code nor the image show any use of Rsubread commands. You don't appear to be doing any alignment, just making a data.frame.

Anyway, there is no R or Bioconductor error called "Killed". "Killed" is an error arising from your operating system, perhaps because you've exceeded your memory quota. It cannot be caused by R commands, except indirectly by using memory.

The hg19 genome is very out of date. It would be far better and more efficient to use Rsubread's inbuilt hg38 annotation.