Search
Question: rsubread exactsnp ERROR "memory not mapped"
0
gravatar for tarek.mohamed
17 months ago by
tarek.mohamed0 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 17 months ago by Wei Shi2.7k • written 17 months ago by tarek.mohamed0
0
gravatar for Wei Shi
17 months ago by
Wei Shi2.7k
Australia
Wei Shi2.7k wrote:

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

ADD COMMENTlink written 17 months ago by Wei Shi2.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 279 users visited in the last hour