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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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abnormal kmer distribution and almost 1T memory #222

Open xunxun66 opened 2 years ago

xunxun66 commented 2 years ago

Hi, @chhylp123

Thank you for this wonderful tool for genome assembly. I have used Hifiasm-0.16.1 (r375) for assembling a Arthropoda genome using about 80G HiFi reads(10X). But I got a abnormal Kmer distribution as the log file attached and now the memory has beed reached to 800G. As we don't have a bigger machine for calculation，do you have any good ideals to deal with this kind of genome assembly? Thank you so much.

hifiasm.log

chhylp123 commented 2 years ago

I guess it is mostly caused by no enough coverage, see: https://hifiasm.readthedocs.io/en/latest/faq.html#why-does-hifiasm-stuck-or-crash .