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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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How to set the cap of RAM used during the ipdSummary process #64

Open uceleste opened 5 years ago

uceleste commented 5 years ago

I'm running ipdSummary using an aligned bam file of about 275 Gb (Aligned.bam) and a fasta genome of about 400 Mb (Assembly.fasta). This is the command line I'm using:

$ ipdSummary Aligned.bam --reference Assembly.fasta --identify m6A,m4C --gff basemods.gff --numWorkers 35

After ten hours of processing the RAM of my machine (128 Gb) got completely saturated and the process shifted to the swap memory, causing a very huge slowdown of the process.

Is there an option to set the cap of RAM to be used or some other option to avoid this problem? I didn't find any specific option regarding the RAM in the help section. Any suggestions?

Thanks