Question: VariantAnnotation: error from readVcf command
1
gravatar for pifferdavide
3.9 years ago by
pifferdavide90
Italy
pifferdavide90 wrote:

I installed the package VariantAnnotation.I followed instructions to run the readVcf command: http://www.bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/inst/doc/VariantAnnotation.pdf

I set the working directory to the folder containing the vcf file and ran the following code. I guess it is telling me that my RAM memory (8gb) is too small to open Chr1?

> library(VariantAnnotation)
> fl <-  ("ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf ")
> vcf <- readVcf(fl, "hg19")
Error: scanVcf: 'Realloc' could not re-allocate memory (5128192000 bytes)
  path: C:\Users\Davide\vcf1\ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf
In addition: Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
  Reached total allocation of 8077Mb: see help(memory.size)
2: In doTryCatch(return(expr), name, parentenv, handler) :
  Reached total allocation of 8077Mb: see help(memory.size)

variantannotation R • 1.3k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by pifferdavide90
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 2.3.0
Traffic: 1528 users visited in the last hour