chhylp123
chhylp123
Could yuu please show the log file?
>When I didn't use "-l 0", I got two haplotype results of about the same size. I guess this is the assembly you are looking for, right? The `-l0` is...
>Is -l 3 used by default? Yes >Why are there no haplotype results when using only hifi data? Could you please double check? I feel like it should be there.
How fragmented it is? If it is too fragmented, there might be some other issues.
If it is tetraploid, then `peak_hom = 17` might be right since it is roughly equal to the coverage per haplotype. For your sample, increasing `-D` to 20 or `-N`...
ERROR6 is a warning. It would be better to wait for the results if hifiasm is still running. Hifiasm might be slow during the final step as your genome is...
But it is still a bit weird. Is it possible that you can share the log file with us?
If hifiasm can take 100% CPU by looking with `top`, it should be fine. It is hard to say for different samples...
It would be better to not run purge_dups for the Hi-C phased assemblies. K-mer evaluation often underestimate the genome size.
Please see: https://hifiasm.readthedocs.io/en/latest/faq.html#why-does-hifiasm-stuck-or-crash. If the coverage is too low, hifiasm cannot find correct peak. In this case, it won't produce results. You could also have a try with the current...