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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Lumpyexpress memory issue #399

Open jordimaggi opened 1 month ago

jordimaggi commented 1 month ago

I have been running lumpyexpress for a year now on WGS human datasets (50X mean coverage, 250 GB of BAM file) wihtout any issues. I am now trying to run it on a larger WGS dataset (460 GB of BAM file), but I run out of memory on chromosome 2. I know there is a region in this chromosome that produces a lot of false positive and has highly increased coverage.

Anyways, I am running the analysis on a dedicated machine with 110 GB RAM allocated to it, and it won't suffice.

Here's the command I am using:

lumpyexpress -B inpu.bam -S splitters.bam -D discordants.bam -o output.vcf -v

Any idea on how to solve this?

Attached you'll find the Exclude file.

Thanks