Mapping 2 wheat genomes

[mfruzan]

I used below command to map one wheat genome against reference in a 32 cpu and 1TByte machine.

minimap2 -x asm5 -f100 -K4g --cs=long -t 32 --secondary=no iwgsc_refseqv2.1_assembly.fa arinalr_sm.fa | paftools.js view -f maf - >cs_arina.maf;

It only uses 6 CPUs, after 3 hours it generated 7Gbyte of maf file (up to chromosome 2) and remained at following line:
[M::main] Version: 2.22-r1105-dirty

Is there any other way to speed up, such as increasing k-mer size or changing -f, or even align each chromosome of query genome one by one?

Thanks ,
Mario

[xbarvazx]

try -f 0.05