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Question: rsubread exactsnp ERROR "memory not mapped"
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gravatar for tarek.mohamed
2.1 years ago by
tarek.mohamed10 wrote:

Hi All,

I am trying to call SNPs from RNAseq data. I am using exactSNP function from Rsubread package. 

I got an error ( *** caught segfault *** address (nil), cause 'memory not mapped')

The script is as follows;

>library(Rsubread)
>exactSNP(SNPAnnotationFile="All_20151104.vcf.gz",readFile="PB01_1_sv.sam",isBAM=FALSE,refGenomeFile="BSgenome.Hsapiens.NCBI.GRCh38.fasta",outputFile="PB01_1_sv.sam.vcf",nthreads=8)

 

 *** caught segfault ***

address (nil), cause 'memory not mapped'

Traceback:
 1: .C("R_SNPcalling_wrapper", as.integer(n), as.character(cmd),     PACKAGE = "Rsubread")
 2: exactSNP(SNPAnnotationFile = "All_20151104.vcf.gz", readFile = "PB01_1_sv.sam",     isBAM = FALSE, refGenomeFile = "BSgenome.Hsapiens.NCBI.GRCh38.fasta",     outputFile = "PB01_1_sv.sam.vcf", nthreads = 8)
aborting ...

 

Thanks,

Tarek

 

ADD COMMENTlink modified 2.1 years ago by Wei Shi2.9k • written 2.1 years ago by tarek.mohamed10
0
gravatar for Wei Shi
2.1 years ago by
Wei Shi2.9k
Australia
Wei Shi2.9k wrote:

You should provide an unzipped VCF file to the 'SNPAnnotationFile' parameter.

ADD COMMENTlink written 2.1 years ago by Wei Shi2.9k
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