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GregoryFaust / samblaster

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
MIT License
221 stars 30 forks source link

Can not run MarkDup for very large bam file #39

Closed liujiayi771 closed 5 years ago

liujiayi771 commented 5 years ago

If I have a very large bam file, the size of the bam file is 129GB. How should I set the parameters of markdup to run it fast? My server has 64 cores, 256G memory. No error is currently reported, but it seems to be just starting, but not running.

GregoryFaust commented 5 years ago

What did you do to fix the problem??