rsubread exactsnp ERROR "memory not mapped"
1
0
Entering edit mode
@tarekmohamed-9489
Last seen 5.2 years ago

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

 

rsubread exactSNP • 1.2k views
ADD COMMENT
0
Entering edit mode
Wei Shi ★ 3.6k
@wei-shi-2183
Last seen 3 days ago
Australia/Melbourne/Olivia Newton-John …

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

ADD COMMENT

Login before adding your answer.

Traffic: 616 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6