Gviz and AnnotateTrack and memory usage
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rejpl ▴ 10
@rejpl-21150
Last seen 4.8 years ago

Hi,

I want to create a AnnotationTrack from a Grange object. However, I got this error "Error: cannot allocate vector of size 1817.1 Gb". My grange contains 493849 rows.

gr
GRanges object with 493849 ranges and 0 metadata columns:
seqnames ranges strand
<rle> <iranges> <rle> [1] chr1 10125-10350 * [2] chr1 564525-564725 * [3] chr1 565225-566100 * [4] chr1 566500-567325 * [5] chr1 567450-567925 * ... ... ... ... [493845] chrX 155229425-155229675 * [493846] chrX 155230050-155231750 * [493847] chrX 155232025-155233400 * [493848] chrX 155233450-155234625 * [493849] chrX 155259700-155259975 *


seqinfo: 23 sequences from an unspecified genome; no seqlengths
DNAseUnionmerged <- AnnotationTrack(gr, name="DNAseUnionmerged", col="#00FFFF", fill='#00FFFF', stacking="dense", chromosome = "chr1")
Error: cannot allocate vector of size 1817.1 Gb

Any help would be appreciated.

Thanks

Jiangyuan

annotation • 498 views
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Vector allocation ERRORs generally mean the data you are trying to create does not fit into your RAM. Depending on what you were doing before this, you might consider doing a gc() (garbage collect) to try and free up space. There is some discussion on these types of issues on stackover flow

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