Question: rsubread exactsnp ERROR "memory not mapped"
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gravatar for tarek.mohamed
2.7 years ago by
tarek.mohamed250
tarek.mohamed250 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

exactsnp rsubread • 873 views
ADD COMMENTlink modified 2.7 years ago by genomax66k • written 2.7 years ago by tarek.mohamed250

With memory errors the first thing to suspect is that you don't have enough available. Have you tried to run this with a smaller number of threads (instead of 8 above)?

ADD REPLYlink written 2.7 years ago by genomax66k

Hi, No I have not, but I am using the university server and I know that these threads are available. Thanks Tarek

ADD REPLYlink written 2.7 years ago by tarek.mohamed250

Hi, I tried it with only 2, and I got the same error

ADD REPLYlink written 2.7 years ago by tarek.mohamed250

Are you allocating a specific amount of memory for the job (is there a default value, especially if you are using a job scheduler)?

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax66k
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