Empty haplotype 2 gfa files by ONT integration

[malearimond]

Hello,
I'm using Hifiasm v0.19 to construct my assemblies based on PacBio Hifi and ONT data using following command:

hifiasm -o ${path}/${ID}_hifiasm_0.19_purged.asm -t 45 --ul ${ONT_data} ${Hifi_data}

I constructed for all of my samples additional assemblies without ONT data as comparison and saw already that using ONT improves the assembly contiguity a lot! But since I'm interested in the different haplotypes, I wanted to have a look at the ${ID}_hifiasm_0.19_ONT_purged.asm.bp.hap1.p_ctg.gfa ${ID}_hifiasm_0.19_ONT_purged.asm.bp.hap2.p_ctg.gfa files.

In the folder without ONT data both were generated, but including ONT resulted in empty ${ID}_hifiasm_0.19_ONT_purged.asm.bp.hap2.p_ctg.gfa files. My samples have an estimated heterozygosity of ~0.9-1.25%. You have any explanation why it couldnt generate hap2 files or have I done something wrong in the command line?

Thanks for your help and best,

Male

[chhylp123]

@malearimond sorry for the late reply. Hifiasm should output two haplotypes with dual assembly. I was wondering if hifiasm has finished successfully for the HiFi+ONT assembly.