big Peak memory of minimap2 in some case when WGS mapping

[wangyugui]

Hi,

big Peak memory of minimap2 in some case when WGS mapping .

For some 1x WGS, the peak memory usage is about 15G, but for some 30x WGS, the peak Memory usage is 40G-60G.

we get the PeakRSS usage with the /usr/bin/time command. /usr/bin/time -f "real\t%e(%E)\nuser\t%U\nsys\t%S\nPeakRSS/K\t%M\n" $@

we can get the memory usage with top command too.

1x wgs result: PeakRSS/K 13757988

30x wgs result: bam.minimap2/ERR1955323/log.minimap2:PeakRSS/K 55838564 bam.minimap2/ERR1955324/log.minimap2:PeakRSS/K 71760960 bam.minimap2/ERR1955325/log.minimap2:PeakRSS/K 65816240 bam.minimap2/ERR1955326/log.minimap2:PeakRSS/K 70995720

bwa have the same problem too. bam.bwa/ERR1955323/log.bwa:PeakRSS/K 45630484 bam.bwa/ERR1955324/log.bwa:PeakRSS/K 51282192 bam.bwa/ERR1955326/log.bwa:PeakRSS/K 41277664 bam.bwa/ERR1955327/log.bwa:PeakRSS/K 60210176

I have tried 'clang -fsanitize=address' but no big memory leak is reported.

minimap2/bwa version:: the last version in github.

I have used top command to get the memory usage of bwa, we can found the memory usage of 10G->30G->9G;

That is to say, there is some case(path) that use too much memory ?

Best Regards Wang Yugui