minimap2 without kmer filter crashes

Question

[Martin]

Hello, I am trying to align pacbio hifi-reads from a dataset to the reference (in may case I use CHM13 data, but this is a general question). I use minimap2 and run following command for the alignment:

 minimap2 -c -x map-hifi -t 32 ref.mmi reads.fastq

The alignment works as intended. But now I would like to see if it makes a difference if I disable the kmer filter or just set it very low. so I run:

 minimap2 -f 0.0 -c -x map-hifi -t 32 ref_new.mmi reads.fastq

\ I experiment with "-f 0.0" an some very low values like "-f 0.00001". I found the flag in the official manual. However, minimap2 crashes for me, if I do this.

Does anyone know why that happens or does anyone have a workaround to run it without kmer filtering?

[Roman]

Please post the input data so we can try to reproduce it.