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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Out of memory #538

Open goblin290272908 opened 11 months ago

goblin290272908 commented 11 months ago

Thank you for providing an excellent tool. I have been using it for genome assembly work. Hifiasm has consistently provided us with assembly results. But in my recent work, we only obtained less than 10X of hifi data for a larger genome (estimated to be larger than 8G, less than 10G), and hifiasm gradually consumed a large amount of memory during runtime until it was killed. Our node has 512GB of memory and 256 threads. Our hifiasm version is 0.16.1-r375. The following is my log file, and I look forward to your reply. thanks again！ log.txt

chhylp123 commented 11 months ago

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 release, which should take less memory than 0.16.1. However, I feel like the best solution is to add more coverage.

goblin290272908 commented 11 months ago

Thank you for giving back so quickly. I will try your suggestion. Thank you very much.