Downside to increasing the number of align buckets?

vpc-ccg / sedef

Identification of segmental duplications in the genome

MIT License

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Downside to increasing the number of align buckets? #16

Closed mrvollger closed 4 years ago

mrvollger commented 4 years ago

Hi,

Is there any downside to increasing the number of align buckets? With my particular assembly the last two align jobs are running for hours after everything else is done so I was hoping to increase the number of buckets to improve full CPU usage.

Thanks! Mitchell

inumanag commented 4 years ago

The only downside is that your file system might not be happy with too many files, so keep the number of buckets <100k. Parameters are currently tuned for hg19, so feel free to adjust them if they do not make sense for other genomes.

mrvollger commented 4 years ago

Great, thanks!