Reducing memory consumption

[cassisnaro]

Hi, I am trying to run the preprocessing step of nebula on a BAM with long reads, in order to later on call it on short read BAMs. However, I am running out of memory: with the entire BED file, 450GB of RAM was not enough. If I take only a fraction of the BED it works, but I am not sure how to then do the merge. Will Nebula consider it as multiple samples? Thanks

[Parsoa]

Hi,

Nebula is not meant to be used and has not been tested with long read (PB or ONT) BAM files with high-error rates. This may result in excessive amounts of kmers being extracted.